The Trouble with TED

An awful of of people seem to waking up to the idea that TED talks are not what they're supposed to be. They attract a lot of kooks who can speak well and exude enthusiasm. How many times have you listened to a TED talk in your area of expertise and wondered how the heck that person got on the stage?

TED talks are just big soundbites and soundbites are not good ways to explain complicated, and potentially revolutionary, ideas.

The NAFTA Superhighway

I just heard about the NAFTA Superhighway. It's going to be as wide as four football fields. Is that Canadian football fields, Mexican football fields, or American football fields?

I can't wait 'till it's finished.

The good news is that I should be able to drive from Toronto to Texas in less than 24 hours.

The bad news is that Texans will be able to drive to Toronto in less than 24 hours.

I hope they have Tim Hortons at the rest stops.

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What Does "pH" Mean?

The term "pH" is used to measure acidity. Strong acids, like hydrochloric acid or sulfuric acid, have very a very low pH while weaker acids, like acetic acid (vinegar), have pH readings that are higher. A "neutral pH" is 7.0, this is close to the pH value of the cytoplasm in living cells.

Higher pH values are "alkaline" rather that acidic. The highest pH value is usually shown as 14 and the lowest pH value is shown as 0.

Acidity is a function of the concentration of hydrogen ions (H⁺), or protons. The strength of alkaline solutions is measured by the concentration of hydroxide ions (OH^-).

There's a reciprocal relationship between the concentrations of these two ions because we're dealing with aqueous solutions (water). Water molecules dissociate into H⁺ and OH^- ions so in pure water there will always be equal concentrations of both ions.

The extent of this dissociation determines the concentration of these ions in pure water. We express the extent of dissociation using a term called the equilibrium constant (K_eq) that is defined as the concentration of the products of a reaction over the concentration of the reactant(s).

For the dissociation of water, the actual equation is ...

Intelligent Design Creationists Attempt to (re)Define Junk DNA

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

On this Day in 1945

Today is the day that the Mars rover Curiosity landed. A remarkable American technological achievement. There have been many other technological achievements in the past century and it's wise to remember them

[reposted from August 6, 2009 (slightly modified)]

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2012 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.

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[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.

The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

Dr. Greg Wells Writes about Athletes and Telomeres

Dr. Greg Wells is a professor in the Faculty of Kinesiology and Physical Education at the University of Toronto. He's the author of Superbodies and he's one of the people commenting on biochemistry on Olympic broadcasts in Canada (see Muscles and the Lactic Acid Myth). It's somewhat unusual to promote yourself as "Dr. Wells" with a Ph.D. in physiology but that's his right.

Here's what he says on his blog,

Greg Wells, Ph.D. is a scientist and physiologist who specializes in health and performance in extreme conditions. Most recently, Dr. Wells was the host of the Gemini-Award winning “Superbodies” segments for Canada’s national Olympic broadcast and the on-camera sport science and sport medicine analyst for the CTV Broadcast Consortium, ABC News and ABC’s 20/20 during the 2010 Vancouver Olympics. Dr. Wells’ on-camera analysis will be a part of CTV’s 2012 Olympic broadcast in London.

Here's one of the "Superbodies" clips that are being shown on Canadian television. Most of them are quite interesting and informative even if Greg Wells does talk about lactic acid from time to time.

I was checking out his blog and found this interesting article: Olympic Science Blog: The science of exercise and ageing.

It is well established that training helps to improve pretty much every organ system in the body including the muscles, blood, brain, nervous system, skin, heart among others. Check out the book "Spark" to read about how exercise can help the brain! But new research shows that exercise can protect our genes as well!

In a recent study, researchers examined the DNA of young and old athletes and healthy control non-smokers for a total of four study groups. As expected, the researchers were able to demonstrate that the athletes had a slower resting heart rate, lower blood pressure and body mass index, and a more favorable cholesterol profile. But the surprising finding was that the rate of accumulated damage to the DNA was much less in the older athletes (average age: 51) than the older healthy non-athletes. In fact, the DNA of the older athletes was “younger” than the younger non-athlete participants. Researchers measured the ends of the chromosomes that contain our DNA. The ends of the chromosomes are called telomeres, and can be thought of as being similar to the caps on the end of your shoelaces (they’re called aglets in case you’re wondering) that prevent the laces from fraying. The scientists who discovered telomeres and how they work won the Nobel Prize in Physiology and Medicine in 2009. Telomeres control the number of times that a chromosome can divide when replicating itself as happens through our lifetime. Cells naturally grow, divide to replicate themselves and then die off. Gradually through this replication process, telomeres shorten and when they become “critically short” the cell dies. On the whole body level this may lead to ageing and a shortened lifespan. Scientists have shown that exercise activates an enzyme called telomerase that protects telomeres and chromosomes and that this has an anti-ageing effect, especially on the cardiovascular system.

World class athletes are training smarter, eating better, and recovering more effectively than ever before. The combination of these factors is helping athletes to have longer and more successful careers. So while you're watching our athletes compete in London and marveling at their performances, think about getting out and doing some exercise yourself! You'll be helping your body - right down to your DNA!

There's a lot wrong with this claim. First, it's not clear that there's a cause-and-effect relationship between telomore length and aging in spite of what some people claim. In fact, the correlation between age and telomere length is barely significant in most studies.

Second, it seems very unlikely that Lamarck was correct and it seems very unlikely that exercise has an effect on expression of the gene for telomerase.

Third, do you suppose it could be possible that when you get older and your health deteriorates for various reasons (disease, aging, accident) you tend not to continue to be an athlete? Thus, the only old athletes you measure are those that are still in good health?

Fourth, what's the evidence that telomere length has more of an effect on the cardiovascular system than on other parts of your body?

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Casey Luskin Wants Us to Categorize Evolution Critics

Casey Luskin has posted an email message that he recently sent to someone who inquired about Intelligent Design Creationism. It describes his view of the debate between Intelligent Design Creationists and scientists [Personal Attacks Against ID Proponents Say More About the Attackers than the Abused].

With that, please let me give you a little introduction to how this debate works. Evolutionists regularly accuse their critics of being "dishonest" and "deceiving." It's a primary tactic they use to respond to criticism and intimidate critics into silence. You're not allowed to dissent from their view and be (a) informed, and (b) honest. Many of them can't fathom the possibility that a person on the other side of the debate could be both.

Here's a fact you might ponder: Virtually every single major person who has criticized the Darwinian viewpoint has faced personal attacks on his or her character. It happens to everyone, myself included. So one of two things are true: Either (1) virtually every single critic of Darwinism (of which there are many) is "dishonest" and "deceiving," or (2) evolutionists habitually respond to scientific challenges with personal attacks.

There's more than two choices here. Let's list the possibilities. Most creationist critics of evolution are ....

1. Uninformed and honest
2. Uniformed and dishonest
3. Informed and honest
4. Informed and dishonest

There are creationist critics of evolution who fit into all categories but category #3 is the least populated. I think Michael Denton and Michael Behe qualify. They seem to have a pretty good knowledge of evolutionary biology and they seem to be sincere in their criticism

Category #4 is tricky. There are some creationist critics of evolution who should be informed but they still say some very silly things. This leads me to suspect that they are being dishonest. Jonathan Wells is a good example.

Categories #1 and #2 contain the vast majority of creationist critics of evolution. They really don't know what they're talking about but it doesn't prevent them from talking. I think most of them are honest IDiots—Casey Luskin is an example and so is Phillip Johnson. Some of them are uniformed and dishonest, that's where I would place Bill Dembski and David Berlinski.

Casey Luskin is wrong when he claims that we accuse all creationist critics of evolution of being dishonest and deceitful. Mostly we just accuse them of being uninformed but acting as if they were.¹ That's probably due to stupidity and not malevolence.

I've left out a huge number of creationists, including the theistic evolutionists who fall mostly into category #3: informed, honest, but wrong.

Where do the rest of them fit in?

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1. Being uninformed is perfectly okay. Most of us are uniformed about a lot of things. You aren't stupid or an idiot just because you don't know something. You become an IDiot when you don't recognize how little you know about a subject but still feel qualified to tell the experts that they are wrong.

Understanding Phylogenetic Trees

A few months ago I posted an exam question from my course on evolution [Exam Question #1]. It was designed to test student's understanding of phylogenetic trees—a serious problem in evolutionary biology. That post generated quite a few comments.

Take a look at this figure from a 2008 issue of Nature. Do you see the problems?

If not, read David Morrison's guest post on Scientipoia: Ambiguity on Phylogenies. He patiently explains all the common misconceptions about phylogenetic trees and references all the important articles in the scientific and pedagogical literature. Once you read his article you will never look at trees the same way again.

You will also be astonished at how bad the scientific literature has become when it comes to explaining phylogenies based on these trees. You would think that evolutionary biologists would have long ago stopped thinking about directions in evolution but it's surprising how often the great chain of being creeps into modern scientific papers.

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[Hat Tip: Mike the Mad Biologist]

Muscles and the Lactic Acid Myth

If you've been watching the Olympics, you've heard the story many times from coaches, athletes, and even team doctors. They all tell you that the performance of endurance athletes is limited by the buildup of lactic acid in their muscles and this is what causes the pain and limits their ability to win a gold medal.

It's the acid that does it and that acid is caused by synthesis of lactic acid taking place during anaerobic exercise, or so the story goes. That happens under extreme conditions when the energy needed by working muscles exceeds the ability to produce it by normal aerobic oxidation. It all sounds so logical ... and so biochemical.

It's all a myth. Lactic acid has nothing to do with acidosis (the buildup of acid in the muscles). In fact, it's not even clear that acidosis is the problem, but let's deal with that another time.

Assuming that acid buildup in muscles is what causes the pain of the long distance runner, where does that acid comes from? In order to answer that question we need a brief lesson on acids.

The Paradox of Stasis?

The word "stasis" entered our consciousness when Gould and Eldredge promoted the concept of punctuated equilibria (see Darwin on Gradualism ). Their observations of the fossil record showed that the morphology of many species remains unchanged for millions of years. Change occurs during speciation by cladogenesis when the new daughter species fixes morphological change, thereby allowing us to recognize it as a different species.

Stasis is an important observation. Here's how Gould describes it in The Structure of Evolutionary Theory (p. 759).

Abrupt appearance may record an absence of information but stasis is data. Eldredge and I became so frustrated by the failure of may colleagues to grasp this evident point—though a quarter century of subsequent debate has finally propelled our claim to general acceptance (while much about punctuated equilibrium remains controversial)—that we ureged the incorporation of this little phrase as a mantra or motto. Say it ten times before breakfast every day for a week, and the argument will surely seep in by osmosis: "stasis is data; stasis is data ..."

Okay, we get it.

What causes stasis? There are many possible explanations. One of the most common is stabilizing selection or the idea that a species is so well-adapted to its environment that any change will be detrimental. According to this view, evolution only occurs when the environment changes.

On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions

It's often quite difficult to imagine how a new enzyme activity could have evolved "from scratch." After all, aren't enzymes highly complex proteins with very specific folds? What's the probability of stringing together just the right amino acids by chance in order to get a new enzyme?

In many cases, new enzymes evolve from primitive enzymes that catalyzed similar reactions [see The Evolution of Enzymes from Promiscuous Precursors]. It's quite easy to see how this could happen by gene duplication and there are tons of examples.

But what about the first primitive enzymes themselves? Presumably, they evolved all on their own. When scientists think of this problem, they usually think in terms of evolving a specific modern enzyme. This looks like a long shot, similar to the probability that a specific person will win the lottery tomorrow. What they don't realize is that this is an unnecessarily restrictive scenario.

Advice to New Creationist Students

We're getting close to the beginning of the semester in the northern hemisphere. That means a lot of high school students will be experiencing university for the first time.

In many cases, students will have graduated from high school with only a rudimentary knowledge of some important topics. This isn't necessarily a bad thing as long as they realize that they still have lots to learn. It becomes a bad thing when they think they know the subject but what they know is wrong.

Universities are places that challenge your beliefs and force you to think. New students should embrace this challenge and look forward to giving up misconceptions and ideas that can't stand up to critical analysis. The last thing you want to do as a new student is to begin university with the idea that your high school ideas are always right.

Which brings us to creationism. A large number of students enter university with little or no knowledge of evolution but they are convinced that it's wrong. They will soon encounter teachers who try to convince them that evolution is true. How should students react to this challenge?

David Klinghoffer¹ proposes one solution on the Intelligent Design Creationist blog Evolution News & Views. Here's his advice [A Piece of Unsolicited Advice to Students].

The practical question is nearly self-answering. You should be very, very circumspect about even hinting at your views to people who will end up giving you grades. But beyond that fairly obvious and uninteresting advice, I wanted to add that you should, in your own mind, strive to give respect to your Darwinist teachers no matter how firmly convinced you are that they are wrong.

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

At an emotional and personal level, I can sympathize with the Darwinist prof who resents his openly Darwin-doubting student. What arrogance, it must seem, to imagine that what I spent decades mastering, you a little pipsqueak think you're ready to discard half-way into the semester. Imagine yourself in your teacher's place. To him, this is about you, in your ignorance and arrogance or at best innocence, sitting in judgment of the system to which he's devoted his professional life.

In other words, hide your views because your professor might punish you. Recognize that your professor thinks he/she knows more than you do but be confident that they're wrong. Realize that when you encounter professors in class they probably don't understand their subject even though they've devoted their lives to studying it. They might be a bit angry if you exposed them so keep you mouth shut.

Above all, resist the temptation to learn and to question your beliefs. You already know the right answer. University is not the a place for learning.

Here's my advice. It you don't want to learn then don't go to university. If your belief in creationism is really strong then don't ever take a biology class—it might turn you into an atheist and your parents will be very upset. If you need the grade, then take the class, but be prepared to fail. It takes courage to openly stand up for what you believe, especially if there might be consequences. But it's the Christian thing to do.

Most professors love it when students challenge their ideas in class. We prefer those kind of students even if they are wrong. You will never fail a course because of your ideas and beliefs as long as they don't conflict directly with scientific facts. If you believe that the Earth is 6000 years old then you will not pass a geology course or a biology, unless you lie. If you dispute the existence of junk DNA then you could get an excellent grade as long as you get your facts correct.

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1. I don't think Klinghoffer has ever been to university. None of the creationist websites mention any university degrees.

Our genome is degenerating, but wait, someone is coming to help us

According to plant geneticist, John Sanford, the human race is degenerating rapidly. It's one of the trade secrets of biology. Every population geneticists knows that it's true.

Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome

Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years?

Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ.

Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?

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[Hat Tip: Uncommon Descent]

Carnival of Evolution #50

This month marks the 50th edition of Carnival of Evolution. The latest version is hosted on Teaching Biology. Read it at: Carnival of Evolution 50: The Teaching Edition

Welcome to the 50th edition of the Carnival of Evolution! In keeping with the name of the blog, this edition will have an educational theme to it. The posts are categorised into modules. Each module has an introduction by me about why it’s important to learn about it, and each post has a short blurb by me on the post’s content and, if appropriate, personal comments. I include a further reading list with links to relevant books and review papers for further discussion/background information. Most of these papers are behind draconian paywalls. If you don’t have institutional access, my e-mail can be found here. Just saying.

I've got seven posts from Sandwalk on the list. That's a record for me and it means one of two things: (a) my posts are getting more interesting, or (b) they were hard up for posts this month.

The next Carnival of Evolution (August) will be hosted by The Stochastic Scientist. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.

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Why Should an Atheist Care About the Problem of Evil?

I am an atheist. What does that mean? It means that I have never seen any evidence that supernatural beings exist. I don't think the devil exists, I don't think that Zeus exists, or Thor, or Gitche Manitou. I don't believe that the god of the Bible exists.

There are thousands of gods that I don't believe in. Some of them have imaginary reputations of cruelty, some of them are supposed to be kind, and some of them are indifferent. It doesn't matter to me because the one thing they all have in common is that they don't exist.

I'm told that some people believe in gods who are supposed to be kind. Those people have trouble understanding why the world is evil. It's a problem that has spawned an entire discipline called theodicy. Bully for them. It's their problem, not mine. I don't accept their premise.

For reasons that seem incomprehensible to me, there are some atheists who really like to talk about the problem of evil as though it were a real problem. Jason Rosenhouse is one of them. You can read his latest at: The Only Reasonable Reply to the Problem of Evil. Jerry Coyne is another. See his post from yesterday at: More Sophisticated Theology: The world’s worst theodicy.

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