Monday's Molecule #192

Last week's molecule was photosystem I (PSI). Mikkel Rasmussen was the only one to get it right [Monday's Molecule #191].

I thought of this week's molecule while I was in Los Angeles last week. We got to sample some excellent examples of cuisine that's hard to find in Toronto. You need to supply the common name AND the formal IUPAC name.

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.

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.)

Evolution and Design

Barry Arrington has a new post on Uncommon Descent in which he discusses design and the appearance of design [Sorry Dr Barr, “Chance By Design” is an Oxymoron]. He's particularly annoyed at someone named Stephen M. Barr, a theistic evolutionary creationist.

Arrington claims that there are only three positions in this debate.

In summary, there are three positions in play here.

(1) The traditional theist observes the overwhelming appearance of design in living things and is content to conclude that things are they way they appear to be, i.e., that living things appear to be designed for a purpose because they are in fact designed for a purpose.

(2) The atheist admits that the appearance of design in living things is overwhelming but asserts that the appearance of design is an illusion and in reality natural law and random chance combine to produce a result that only appears to be designed.

(3) The Barr-type theistic evolutionist admits that the appearance of design in living things is overwhelming but asserts — like the atheist — that the appearance of design is an illusion and in reality natural law and random chance combine to produce a result that only appears to be designed. The TE then goes one step further by asserting that the explanation of the illusion of design is itself an illusion, because the randomness of evolution is in fact directed.

This isn't correct. I support the 4th position; namely ....

(4) When you step back and look at the big picture, living things do not appear to be designed and they do not appear to have a purpose. While there may be some features of living things that have been honed by natural selection, they are the exception, not the rule. Even those features with a strong illusion of design look much less designed when you examine them closely.

When I talk about Evolution by Accident I intend that to be an attack on Intelligent Design and also an attack on the Dawkins' view of evolution.

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J. William Schopf Wins Paleontological Society Medal

I read this on the National Center for Science Education (NCSE) blog [Congratulations to J. William Schopf].

NCSE is delighted to congratulate J. William Schopf on receiving the Paleontological Society Medal, the most prestigious honor bestowed by the Paleontological Society, on November 4, 2012, at the Geological Society of America's annual meeting. A life member of NCSE, Schopf is Professor of Paleobiology in the Department of Earth and Space Sciences at the University of California, Los Angeles, and the author of Cradle of Life: The Discovery of Earth's Earliest Fossils (Princeton University Press, 1999). Previous recipients of the medal include NCSE Supporters Niles Eldredge, Stephen Jay Gould, and Malcolm C. McKenna.

I'm quite surprised by this award since Schopf's main claim to fame is the discovery of fossil cyanobacteria in Australian deposits that date back 3.45 billion years. These "fossils" are definitely not cyanobacteria and they most likely aren't even fossils [Did Life Arise 3.5 Billion Years Ago?.

Does anyone know more about this award? Does the paleontological society still believe that these "fossils" are actually ancient bacteria or was the medal awarded for some other contribution to paleontology?

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Michael Behe in Toronto!

Michael Behe is giving a talk on Thursday evening at 7:00pm in rm 3154, Medical Sciences Building on the campus of the University of Toronto. (The lecture room is just two floors below my office.)

There's also a reception for him at Hart House on Thursday afternoon. Let me know if you plan to attend either event. Maybe we can meet for dinner.

The talk on Thursday evening is on "What Are the Limits of Darwinism?" I assume he's going to talk abut irreducible complexity and the edge of evolution. Neither topic is suitable for discussion during question period. I think I'll ask him to explain how common descent is compatible with the actions of an intelligent designer.

Is Intelligent Design Scientific?

Intelligent Design is often dismissed as unscientific because it violates various criteria used to define "science." One of the restrictions imposed upon science by some philosophers is "methodological naturalism." This rules out any hypothesis that invokes a non-materialistic cause such as an intelligent designer.

I reject that limitation on science as a way of knowing. Are there any other reasonable definitions of "science" that can be used to exclude Intelligent Design while still including other hypotheses that we'd like to keep?

Here's Stephen Myer arguing that the answer is "no." Is this a good argument? Note that I'm not asking whether you agree with intelligent design. I'm simply asking whether there's a good argument for dismissing it as nonscientific and, therefore. should never be discussed in a science class. If you think the answer is "yes" then please give a definition of "science" that excludes Intelligent Design but includes speculations on the origin of life, string theory, and whether Bigfoot exists.

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The Central Dogma Dies Again! (not)

You expect IDiots to be idiots so it's not surprising that they consistently screw up their analyses of scientific papers. The latest is a post by David Taylor on the Central Dogma of Molecular Biology [Revisiting the Cental Dogma] [Revisiting the Central Dogma]. He has just noticed a paper published in 2011 where two scientists challenge the Central Dogma. Naturally, this is interpreted to mean that Intelligent Design Creationism is true.

It's frustrating to read yet another scientific paper announcing the demise of the Central Dogma of Molecular Biology. If you've been following the literature, you'll know that the Central Dogma is regularly killed off about ten times per year—a rate that's been fairly constant for thirty years. But to paraphrase Mark Twain, reports of the death of the Central Dogma are greatly exaggerated.

Let's look at the paper by Sarah Franklin and Thomas M. Vondriska from the David Geffen School of Medicine in Los Angeles California (USA) (Franklin and Vondriska 2011). This is a paper that specifically addresses the Central Dogma of Molecular Biology so you'd expect that the authors understand what they are attacking, right?

A New Grandson

Luca Gerard Tarabokia was born early on Sunday morning. He's named after Michael's great grandfather, Luca Tarabokia, who came to America almost one hundred years ago from an island in the Adriatic Sea (now Croatia). Here's a photo of Luca with his mother (my daughter), Jane, and his big sister Zoë.

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A Halloween Witch

We're in Venice, California (USA) (near the beach to the west of Los Angeles) awaiting the birth of our grandson. Last night we went trick or treating with granddaughter Zoë. She loved her witch costume and she applied her makeup all by herself.

Halloween is a very big deal in Venice—probably because it's so "bohemian/hippie." There were hundreds of kids in the streets and most houses had elaborate Halloween displays that have been up for days (see And Now for the Spookey Part, and Halloween in the Hood).

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The Stockbridge 14: What Did They Discover?

Fourteen people have been invited to a special meeting in Stockbridge Massachusetts (USA). They are: Sean Carroll, Jerry Coyne, Richard Dawkins, Terrence Deacon, Simon DeDeo, Dan Dennett, Owen Flanagan, Rebecca Goldstein, Janna Levin, David Poeppel, Alex Rosenberg, Don Ross, Steven Weinberg, and Massimo Pigliucci. On the first day they discussed "naturalism" (morning session) and evolution, complexity and emergence (afternoon session"). Read the summaries in the links to my first post [The Stockbridge 14].

What Is Critical Thinking?

We all use the term "critical thinking to describe one of the primary goals of education. What do we mean by "critical thinking"?

As usual, it takes a philosopher to sort out the various meanings and arrive at a reasonable definition. (Philosophers are experts at critical thinking, although they often use it when it's not necessary.) Read what John Wilkins has to say at: What is critical thinking. Contrast his critical thinking about the subject with that illustrated in the Wikipedia article on Critical Thinking.

Here's his bottom line but you really need to see his examples of what is not critical thinking.

Critical thinking is the application of careful analysis and rational reconstruction to arguments, so that the correctness of the reasoning and the truth of the premises can be evaluated and the support for the conclusion determined.

Rational thinking is the assent of the reasoner to any conclusion that is both correctly reasoned and founded on known to be true, or likely to be true, premises.

In short, a critical and rational thinker is one who accepts the conclusions of good arguments.

I agree with John and this is what Chris DiCarlo and I teach in our course. But, you should read the comments on John's blog.

Once you've mastered the basic rules of logic, most arguments should be about whether the premises are likely to be true.

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The Stockbridge 14

Fourteen people have been invited to a special meeting in Stockbridge Massachusetts (USA). They are: Sean Carroll, Jerry Coyne, Richard Dawkins, Terrence Deacon, Simon DeDeo, Dan Dennett, Owen Flanagan, Rebecca Goldstein, Janna Levin, David Poeppel, Alex Rosenberg, Don Ross, Steven Weinberg, and Massimo Pigliucci. So far they've discussed the meaning of "naturalism," including the nature of reality (morning session) and evolution, complexity and emergence (afternoon session") [Moving Naturalism Forward].

You can read Jerry Coyne's description at: Interim report: Moving Naturalism Forward Meeting. Massimo Pigliucci has also written about the first day at: From the naturalism workshop, part I.

So far it sounds quite boring. It looks looks like some of the philosophers have tricked the scientists into debating the precise meaning of words that nobody has been able to define precisely in the past one hundred years. Does anyone outside of philosophers actually care whether we have precise definitions of "naturalism" and "supernatural"? We all know what we're talking about when we discuss the existence of god(s).

And what about "emerging properties"? Surely that's a topic that's already been debated to death? What in the world do they expect to learn other than the fact they disagree on the definition of what an enregent property actually means?

As for complexity, it's either so simple that we all recognize it when we see it, or so "complex" that nobody cares. Here's what Coyne says ...

The discussion of complexity, introduced by Simon DeDeo and much discussed by Janna Levin, was way over my head. I found some consolation in the fact that Dennett, too, announced that he didn’t understand what was being said!

That doesn't sound very promising.

I'm not looking forward to the results of the next two days because they're going to tackle silly topics like the nature of morality, free will, "meaning," and "purpose". I wonder if they're going to debate the difference between methodological naturalism and philosophical naturalism? I wonder when they'll get to the issues of how many angels can dance on the head of a pin?

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[Photo Credit: One Angel Dancing on the Head of a Pin]

Five Myths (?) About Intelligent Design Creationism

Melissa Travis writes for a blog called Hard-Core Christianity. Her latest post is: Top Five Myths Christians (and Non-Christians) Often Believe About Intelligent Design. It's interesting because it reveals the standard myths that Intelligent Design Creationists believe about themselves.

Here's the list of "myths" along with what Mellisa Travis has to say about them.

MYTH #1: Intelligent Design (ID) is just a fancy name for Creationism.

The true story: Intelligent Design theory is not a form of, nor is it synonymous with “creationism.” Rather, it is an over-arching scientific theory that disputes wholly naturalistic/materialistic accounts of the origin of the universe and the origin of life. As such it is an indispensable ally for those who espouse various creation models. ID makes NO CLAIM about the age of the earth.

FACT: Modern Intelligent Design Creationism evolved from the creationist movement in the 1980s as was proven conclusively in the Dover trial. Intelligent Design Creationism is not a scientific theory. Instead, its a hodgepodge of criticisms of evolution and of scientists and materialism. Just look at the posts on Evolution News & Views (sic) to see what it's all about. Count the number of posts promoting a "scientific" view of Intelligent Design Creationism as opposed to disjointed helter-skelter criticisms of evolution that often contradict each other.

There's no "over-arching" scientific theory in sight.

Is It True?

Is it True? Uncovering the Heart of Each of the World's Religions

The University of Toronto Secular alliance (UTSA), in conjunction with Power 2 Change, Muslim Students Association and the Multifaith Centre is hosting a lecture and discussion series entitled "…is it true?"

This series will feature the following speakers:

Oct. 24: Islam (Amjad Tarsin, Muslim Chaplain, U of T)
Oct. 31: Christianity (Kyle Hackmann, Grace Toronto Church)
Nov. 7: Judaism (Yishaya Rose, Chaplain, Chabad House, U of T)
Nov. 14: Atheism (Professor Larry Moran, U of T, Secular Alliance)

Each speaker will speak on behalf of the philosophical framework to which they subscribe to. Following the lecture, there will be a period of Q and A following by an open discussion amongst attendees.

I encourage you to attend these talks as I suspect a lot of fruitful conversations can emerge. To this end, specifically, we are delighted to have biochemist Dr. Larry Moran, represent our side of the conversation.

University College 5:30pm-7:00pm, rm 52. Light dinner will be served.

Please find event page below:

Facebook

Hope to see some of you there!

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Monday's Molecule #191

Last week's molecule was L-dopa. The winner was Raul A. Félix de Sousa (again, but this time only by four minutes!) [Monday's Molecule #190].

This week's molecule is much more complicated and it's also much more important. You need to identify this complex making sure you distinguish it from other similar complexes. You don't need to name the exact species but you should have some idea of which organisms have this complex and which ones don't. There's not enough room in the comments for the complete IUPAC name!

You'll get special bonus points (and the expensive lunch in the dining room instead of the pub) for explaining how an irreducibly complex structure like this could have evolved.

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.

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.)

Stupid American Atheists

American Atheists have decided that it's in their best interests to take sides in the Presidential election. They produced a billboard and mounted it on a truck to drive around Boca Raton, Florida, the site of this evening's third presidential debate [American Atheists Demand Answers on Romney's Religious Loyalty].

This is not only an attack on religion—as opposed to an attack on the existence of god(s)—but it's an attack on a particular religion that just happens to be the religion of one of the candidates. There's no balanced attack on the religion of the other candidate even though his religion is just as bad.

This is really stupid and American Atheists should be ashamed of themselves. It's the sort of thing that rightly fuels the accommodationist objections to the New Atheists.

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