Friday, August 3, 2012

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.

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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.

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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.


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

Wednesday, August 1, 2012

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?



[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.

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.


They Like Me, They Really Like Me!

Well, maybe not all the IDiots really like me but David Klinghoffer is sure a big fan [You Go, Larry Moran!]
Just think. Imagine you're one of those undecided fence-sitters on the Darwin question that he thinks he's appealing to. Or say you're a journalist, reflexively pro-Darwin but one who's never had an occasion to follow the controversy in the past. Now something's come up in the news that touches on evolution and you figure you'll sample the arguments on both sides with a view to writing on it.

You stumble upon the blog, named in honor of Charles Darwin's famous "Sandwalk," of a University of Toronto biochemist and man of mature years who writes this way, over and over and over. He will, for example, reproduce a photo of an Internet Darwin critic with the words "I'm an IDiot" superimposed. This same biochemistry professor and Darwin advocate writes blog posts trying to defend and recommend this approach, including his favorite term "IDiot," to others. Are you impressed? That's a self-answering question.

Of course it would be different if Moran were not a guy who teaches in a relevant scientific field at a university you've heard of. If he were just another one of those pseudonyms that populate comment boxes around the Internet, and who dish out their own vicious/viscous stuff, no one would care. Much as it's distasteful to read Moran's blog (as I very rarely do), there's reason to be grateful for its existence.

Now watch, he's going to trawl the Internet for a picture of me and write "I'm an IDiot" on it and post that.

If I were purely strategic, I would say: Give us more, Larry Moran! Pour it on. Please!
Happy to oblige.