The Hobbit Is Coming to Toronto

The hobbit is coming to Toronto. I knocked on the door but there was no answer.

He's not here yet.

Can't wait to meet him.

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[Photo Credit: I took this picture in the commuter train concourse at Union Station, Toronto, Ontario, Canada]

Breaking News: IDiots Don't Understand Genomes or Biology

Just when you think they couldn't get more stupid, along comes some IDiot to prove you wrong. Here's the latest from an anonymous contributor at Evolution News & Views [Your Genome? Which One?].

A new finding about DNA differences in somatic cells overthrows a common assumption and might have dramatic implications for evolutionary studies.

Young's Law (from Murphy's catalog of perverse tendencies in nature) states that all great discoveries are made by mistake. A corollary is that the greater the funding, the longer it takes to make the mistake, but we won't go there. Anyway, a team of Yale scientists wasn't looking to overturn a huge assumption in genetics -- but they did. The ripple effects of their discovery remain to be seen.

We've all been told that every cell in our body has a copy of our unique genetic code. That's one of those simplistic beliefs that sounds sensible but is almost impossible to check. Doesn't the whole body arise from cell divisions of a single zygote with its unique genetic code? Yes, but it doesn't necessarily follow that the genes in cells downstream don't get modified. That was just assumed....

"Somatic mosaicism" is jargon for the finding that genomes differ from cell to cell -- not only in copy number variations (CNV's), but in single nucleotide polymorphisms (SNP's). The assumption that you have one genome is thus falsified. You have lots of genomes!

Okay, let's take a poll.

How many of you thought that mutations such as nucleotide substitutions, deletions, and insertions, could never take place during the thousands of generations that give rise to our somatic cells? (How were they supposed to be suppressed?)

How many of you thought that all of our cells, including red blood cells, contain copies of our unmodified genome?

How many of you thought that there were no polyploid cells in our liver?

How many of you thought that B cells, and T cells (and others) contain the same identical copy of our genome that's found in germ cells?

How many of you thought that spermatocytes and ovaries have exactly the same genome as our original zygote?

How many of you thought that cancer-causing gene rearrangements and mutations in somatic cells were impossible?

How many of you are completely ignorant of any medical problems due to genetic mosaicism?

If you answered "yes" to all of those questions then, congratulations!, you're as smart as an IDiot.

Sheeesh!

One thing is clear at this stage: the assumption that each individual has a unique genome has been overthrown to some extent. Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? Remember, the Yale team found differences between cells in the same organ -- human skin. If the percent difference grows or shrinks depending on the source, any conclusions about human-chimp similarities would prove unreliable.

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I Get Mentioned, Again, on an IDiot Blog

The nameless people at Evolution News & Views (sic) didn't like my comments about Michael Behe. Naturally they focus right in on defending the IDiot science (not!) [Giving Thanks for Minority Opinions]. (The reference to "thanks" is in honor of today's American Thanksgiving holiday.)

When in the future they write the history of modern biology, if it turns out that contemporary ID theorists were onto something big, then Michael Behe's name will figure very prominently as one who helped launch the intelligent-design revolution.

When that history is written, whatever fate holds in store for ID, no one thinks that University of Toronto biochemist Larry Moran's name will figure prominently in any account as a thinker of great stature or influence.

So there's some irony in Moran's patronizing three-part series, at his blog Sandwalk blog, about meeting Mike Behe when the latter came to visit and speak recently in Toronto. Moran is full of condescension and, sticking to the science as always, carefully points out the discrepancy in physical stature between himself and Behe where Moran does have the advantage -- "He's a lot shorter than I imagined but otherwise looks just like his photos." Moran includes a photo of himself leaning over Behe with a smirk to prove the point. Well then!

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Elisabeth Lloyd: Gould and adaptation: San Marco 33 years later

This is a talk by Elizabeth Lloyd from a conference in Italy last May on "Stephen J. Gould’s Legacy: Nature, History, Society." Thanks to Ryan Gregory for posting all the videos [Stephen Jay Gould conference in Italy — full series of talks].

Lloyd explains the problems with the adaptationist approach to the logic of research questions using a case study on the evolutionary origins of female orgasm. She points out that Gould & Lewontin were right 33 years ago when they called attention to the adaptationist bias and that things haven't changed very much.

This is an excellent example of a philosopher of biology, Elizabeth Lloyd, making a substantial contribution to science and the philosophy of science

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Dennis Markuze Arrested, Again

From The Gazette (Montreal, Quebec, Canada): Man charged with threatening people using social media — again.

A Saint-Laurent man has been charged, again, with abusing social media to threaten people who express their views online.

Dennis Markuze, 40, faces three new charges, including one alleging he violated the conditions of a sentence he received in May for the same offence. He was also charged with threatening the Montreal police officer who was investigating claims from several of Markuze’s past victims. Those victims alleged that Markuze’s threats have intensified in recent months.

In May, Markuze received an 18-month suspended sentence after pleading guilty to uttering threats toward eight people he believed to be atheists. The court was told Markuze’s problems could be attributed to drug consumption, which caused him to believe he was “the Voice of God.” As part of his sentence, he was ordered to “abstain from participating in a social network, blog and discussion forum.” But during the summer, several people contacted The Gazette to report that Markuze appeared to be ignoring the court order.

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[Hat Tip: Friendly Atheist]

Michael Behe in Toronto: Part 3

I went to three of Michael Behe's talk while he was in Toronto [see Michael Behe in Toronto!, Part 1,
Part 2].

The third talk was on Friday morning (Nov. 15, 2012) in the Multifaith Centre. It was sponsored by Power to Change (formerly Campus Crusade for Christ). There were about 150 people in the audience, mostly undergraduates. I estimate that less than half were believers.

Behe gave pretty much the same talk he had given the night before. There was only time for a few questions and most of them were from skeptics. Two students challenged the science but their questions were convoluted and confusing and Behe had no trouble dismissing them. (The standard trick is to say "That's a very good question" and then suggest they could discuss it later on so that others have a chance to ask questions right now.)

One student asked about the philosophical justification for some of Behe's conclusions. It was a valid question but way over the heads of the audience. Behe gave an incorrect answer. I spoke to that student and her friends after the talk. Several of them were taking biology/evolution courses but they weren't really prepared to identify the flaws in Behe's arguments. They just knew that he had to be wrong.

This is the problem. It's just not that easy for the average person to refute the arguments of people like Michael Behe and Jonathan Wells. That's why we need to teach the controversy in school and show why their science is flawed.

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My Posts on Michael Behe

Here's a bunch of posts that I've done over the years on Michael Behe and his ideas about evolution. I'm putting them here so I don't have to repeat myself, again.

Understanding Mutation Rates and Evolution

The Edge of Evolution

Evolution in Action and Michael Behe's Reaction

Mutations and Complex Adaptations

Blown Out of the Water

Joe Thornton vs Michael Behe

Irreducible Compexity

Defining Irreducible Complexity

Another Bad Review of The Edge of Evolution

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The Discovery Institute Presents the Case for Magic

Here's a propaganda video produced by the Discovery Institute. It's based on a book called The Magician's Twin edited by John G. West. John G. West is "a Senior Fellow at the Seattle-based Discovery Institute (DI), and Associate Director and Vice President for Public Policy and Legal Affairs of its Center for Science and Culture (CSC), which serves as the main hub of the Intelligent design movement."

In other words, he's one of the chief IDiots.

The video is interesting for several reasons. Not only does it have the look and feel of a 1950's American propaganda film but it mimics the same utter lack of critical thinking that characterized that genre of film. Perhaps this is intentional since the goal is to attack rationality and critical thinking and the last thing you want to do is be accused of using the very tools that lead to evils such as eugenics, evolution, atheism, and Marxism. (But see "doublethink," below.)

Michael Behe in Toronto: Part 2

Behe's main talk was last Thursday evening at 7pm (Nov. 15, 2012). It was in the lecture theater were we teach medical students. The room holds about 350 students and every seat was taken. There were about 100 people sitting in the aisles and on the floor.

The gist of Behe's talk was that "Darwinism" can't explain macroevolution. The problem isn't common descent—Behe agrees that common descent is "trivial." The problem isn't natural selection—Behe doesn't have a problem with natural selection. The problem is random mutation. It's incapable of generating the required changes in a timely manner.

Monday's Molecule #193

Last week's molecule was capsaicin, the molecule responsible for the "hot" sensation of chili peppers. There were two winners: Seth Kasowitz and Bill Gunn [Monday's Molecule #192].

This week's molecule is featured in an article that I will (hopefully) blog about in the next few days. There's a common name of sorts but you will need to supply the correct IUPAC name to win the free lunch.

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.)

Michael Behe In Toronto: Part 1

Michael Behe was in Toronto last Thursday and Friday (Nov. 15 & 16, 2012). His visit was sponsored in part by the Copernicus Group, a group of Christian men who are interested in the dispute between science and religion. I met several of them (three physicians and an engineer).

The first of Behe's talks was organized by the Copernicus Group who invited faculty and graduate students from the Dept. of Biochemistry and the Dept. of Molecular Genetics to a session at Hart House in the afternoon. Only eleven people showed up—four (five?) of them were from the Copernicus group. There were ten bottles of wine!

This was the first time I had a chance to meet Michael Behe in person. He's a lot shorter than I imagined but otherwise looks just like his photos.

Waiting for Santa

Today's the day of the Santa Claus parade in Toronto. The radio tells me that one million people will be lining the parade route when the parade begins. Here's the Santa Claus fans just outside my building on Queen's Park Circle. You can see that some of them were smart enough to bring a Tim Hortons coffee.

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Ann Gauger Says Random Mutation Can't Possibly Account for Observed Evolution

The Intelligent Design Creationists change their stories so often that it's sometimes hard to keep up. The latest rationalization has to do with the sufficiency of random mutations. Here's the version given by Ann Gauger, Senior Research Scientist at Biologic Institute.

There's a lot of discussion about this video on the Biologic Facebook page [Biologic Institute]. Some commenters (e.g. Nick Matzke) raise the issue of neutral mutations and Gauger responds (not very well). This is one of the main problems with the current IDiot propaganda. They confuse the probability of specific, single nucleotide, beneficial, mutations at a specific binding site—which have a low probability—with the total number of possible mutations at thousands of different sites, any of which could have an effect on development. Many of the mutations could have been neutral giving rise to an enormous amount of standing variation in the population. (This makes it much more likely that you will get multiple mutations.)

Don't forget we're looking at a specific outcome (evolution of Homo sapiens from a common ancestors over 6 million years). There were thousand and thousands of other possible outcomes that could have given rise to intelligent beings (maybe smart chimps?) who would eventually spawn Intelligent Design Creationists.¹ We don't know the total number of possibilities but it certainly isn't just one (1). Our species is a lottery winner and we all know that specific lottery winners are highly improbable.

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1. I wonder if there are any possible pathways that would have given rise to truly intelligent beings and no IDiots?

Is It Science?

I've been having discussion with several of my friends and colleagues about whether the activities of the Intelligent Design Creationists count as "science." My position is that much of what they do is science, especially when they criticize existing scientific explanations. It may not be very good science but that's not the question. After all, there are atheist scientists who don't do much better.

One argument is that simply criticizing current theories doesn't count as science unless you can also offer a plausible, scientific, competing model. I don't think that's a requirement. Here's an example we can discuss ...

One of the latest posts on Evolution News & Views (sic) is an article by Casey Luskin criticizing the old Urey-Miller experiment by pointing out that their origninal conditions didn't mimic the conditions on the primitive Earth [On the Miller-Urey Experiment, Wikipedia Offers a Citation Bluff]. He goes on to say that scientists still haven't shown convincingly that amino acids (and other molecules) could have formed spontaneously on Earth. Furthermore, the "chirality problem" hasn't been solved.¹

Luskin correctly points out that a Wikipedia reference misrepresents the science it reports.

Is this (Luskin's article) scientific? Isn't criticism of current models and hypotheses an example of how science is supposed to work?

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1. I agree that the spontaneous formation on Earth of significant amounts of amino acids, carbohydrates, and, especially, nucleotides, is extremely unlikely. That's why I support "Metabolism First." I disagree about the chirality problem—I think we have a good explanation.

The Most Spectacular Mutation in Recent Human History

Benjamin Phelan is a writer. He has an article in Slate on The Most Spectacular Mutation in Recent Human History.

I'm not going to tell you what it is. You'll have to read his article. But here are a few hints.

1. The mutation is only common in Europeans. Asians and Africans get along just fine without it.
2. It's not clear whether the mutation confers selective advantage. There's some evidence that it does but it's difficult to understand why.
3. There are several different mutations that produce the same phenotype and it's not clear which one of them is the "most spectacular."
4. The article claims that the mutation appeared 10,000 years ago but that's probably not true.
5. The mutation has nothing to do with walking upright, opposable thumbs, big brains, or the ability to talk. Apparently those mutations are either much less spectacular or they don't qualify as "recent."

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[Photo Credit: How to Milk a Cow]
[Hat Tip: Mike the Mad Biologist]

Happy Birthday Gord!

Today is my son's birthday. Here's two pictures of him taken 34 years apart.

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Is It True? Today at 5:30pm

The Multifaith Centre at the University of Toronto is sponsoring a series of talks. I represent the control group (no faith).

The title of the series is "Is It True?" Tonight I will defend the negative position from 5:30-7:00pm in room 52 University College. If you're in Toronto, come out and participate.

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 #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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Chris Stedman Defends Accommodationism

Chris Stedman is currently the Assistant Humanist Chaplain¹ and the Values in Action Coordinator for the Humanist Community at Harvard [Chris Stedman]. He has a Master's degree in religion and is a former evangelical Christian.

As you might imagine from his position at Harvard, Stedman supports the non-theistic Humanism "religion." His goal is to advance particular social policies and often that goal is shared by theists. Hence, cooperating with theists to achieve common goals, such as social justice, is a major part of his life.

That's noble. Even though I don't share his humanist worldview—and have no intention of becoming a humanist—I can support many of the issues he is passionate about. Like all my atheist friends, I have no problem working with theists of all stripes when it comes to making our society a better place—just as I have no problem working with conservatives, homeopaths, anti-abortionists, people who favor capital punishment, pro-gun lobbyists, and even misogynists and racists if the issue is important enough.

Another Evolutionary Paradox?

The IDiots are remarkably good at uncritical thinking. When you couple this tendency to ignorance of evolution, you come up with some remarkable conclusions.

Take, for example, the well-known fact that rich people tend to have fewer children than poor people. What this means is that poor people are better at passing on their genes (alleles) to the next generation than rich people. If there is a genetic component to richness and poorness then poor people are "more fit" than rich people and, eventually, the poorness alleles will become fixed in the population. That's just a fact and it doesn't matter what you might think about the genetic advantage of being rich.

Of course there may not be any significant difference in the genetic compositions of rich people and poor people in which case the argument becomes moot.

Let's see how an anonymous IDiot deals with this information on their main blog site, Evolution News & Views (sic) ... [Survival of the Poorest: Another Evolutionary Paradox].

Here's another evolutionary paradox: the "demographic transition." We've alluded to this before, but why not recall the point? Darwin notwithstanding, it seems to support the view that the meek shall inherit the earth.

By all accounts, the rich should be, in Darwinian terms, the fittest. They have the most resources, and the most opportunities for advancement. Yet they leave fewer offspring. That's the finding of a large study of Swedish families that's just been completed.

Nature recently recognized that this has been a known contradiction to evolutionary theory.

"Fitness" is defined in all evolutionary biology textbooks as ...

The fitness of a genotype is the average lifetime contribution of individuals of that genotype to the population after one or more generations ... A general term for this number is reproductive success, which includes not simply the average number of offspring produced by the reproductive process, but the number that survive, since survival is prerequisite to reproduction.

Futuyma, D.J. (2009) Evolution p. 306

Do the IDiots ever read basic introductory evolution textbooks or do they just pull out "evolutionary paradoxes" from their nether parts? There's no contradiction with evolutionary theory and there's nothing in "Darwinian terms" that defines fitness as anything but reproductive success.

The only "puzzle" might be the naive presumption that rich people should have more reproductive success than poor people but we've known that this isn't true for over one hundred years.

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[Photo Credit: Ten children of Ethel and Bobby Kennedy (the 11th child was born after Bobby was killed). This is the exception that proves the rule. Prompted by last night's viewing of the remarkable documentary Ethel which also prompts the question, "Why doesn't America have principled politicians like Bobby Kennedy any more?"]

Science Journal Publishes More Gobbledygook

I don't know what's happening at Science these days. It got caught up in the arsenic affair last year and it recently made a fool of itself over the ENCODE publicity fiasco where it was completely duped by Ewan Birney.

Now it has published the following "perspective" in the October 12th issue. It reads like a Sokal hoax but it's perfectly legitimate. That's actually how Stuart Neuman proposes to solve the mystery of the Cambrian explosion.

Stuart A. Newman
Physico-Genetic Determinants in the Evolution of Development
Science 338:217-219 [DOI: 10.1126/science.1222003]
Abstract

Animal bodies and the embryos that generate them exhibit an assortment of stereotypic morphological motifs that first appeared more than half a billion years ago. During development, cells arrange themselves into tissues with interior cavities and multiple layers with immiscible boundaries, containing patterned arrangements of cell types. These tissues go on to elongate, fold, segment, and form appendages. Their motifs are similar to the outcomes of physical processes generic to condensed, chemically excitable, viscoelastic materials, although the embryonic mechanisms that generate them are typically much more complex. I propose that the origins of animal development lay in the mobilization of physical organizational effects that resulted when certain gene products of single-celled ancestors came to operate on the spatial scale of multicellular aggregates.

Neuman was one of the Alternberg 16, a group of scientists who met in Altenberg, Austria in 2008. Their purpose was to develop a new theory of evolution. The proceedings were collected in a book edited by Massimo Pigliucci and Gerd B. M^uuml;ller, Evolution: The Extended Synthesis.

This story has been promoted by a rogue journalist named Suzan Mazur and she has written a book on the subject. Here's her interview with Stuart Newman, The New Master Of Evolution?. Elizabeth Pennisi, a senior editor at Science, helped publicize the Altenberg 16 back in 2008 by publishing an article in Science [Modernizing the Modern Synthesis]. She has been sympathetic to the bizarre views of some Altenberg 16 members so I suspect she's behind the publication of Stuart Newman's article in Science.

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Douglas Axe on Protein Evolution and Magic Numbers

Imagine that I asked you to "prove" evolution by transforming a chimpanzee into a human. Would you recognize the fallacy that I described recently in Why Are Chimps Still Chimps?. Of course you would. Any intelligent person who understands evolution knows that chimps and humans share a common ancestor and both have evolved substantially since the two lineages diverged. In order to change a chimp into a human you would first have to "devolve" it back to the common ancestor and proceed from there. That requires a lot of changes.

Now let's think about two enzymes that are members of the same gene family but have evolved different functions. It's easiest to think of these as two enzymes that are now specific for similar but distinct substrates. Imagine that you were asked to "prove" evolution by changing one of those enzymes into the other? Would you recognize the same fallacy? Would you realize that the most likely evolutionary scenario is that the two different enzyme specificities evolved from an ancestral enzyme that carried out both reactions? [see: The Evolution of Enzymes from Promiscuous Precursors]

Changing one of the modern enzymes into the other would require many changes because in most cases the common ancestor dates back hundreds of millions of years. Many of the changes that have become fixed in the two lineages were not directly involved in selecting one of the substrates over the other (i.e. increasing specificity). They were neutral mutations fixed by random genetic drift after the enzyme became specialized for one or other of the substrates. Many would have to be "reversed" in order to re-create the dual specificity because they would have been detrimental in the ancestral enzyme.

Think about these facts as you watch Douglas Axe explain why his research shows that evolution is impossible [Video: Doug Axe on Protein Evolution's Magic Number (It's Six)].

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On Attacking the Integrity of Scientists

We are discussing the evolution/creation controversy in my course. One of the issues that comes up frequently is the role of scientific evidence. The importance of science in the 21st century cannot be exaggerated. Everyone wants science to be on their side because if your views conflict directly with scientific evidence then your case is very weak.

So, how do creationists handle this issue? They usually try to present counter-evidence or they cherry-pick the scientific literature looking for papers that lend support to their cause. But that only takes you so far. Creationists are forced to admit that the vast majority of scientists support evolution and that's a real problem for their flock.

The solution is obvious. If you can't attack the science then attack the scientists. By casting doubt on the motives of scientists you can partially neutralize the impact of science.

Here's an excellent example from today's post on Evolution News & Views (sic) [How to Talk About "Evolution"].

Better to think of opinion as sharply divided. The professors, their students and many university-educated people believe one thing (evolution is a fact) and most everyone else is suspicious. They won't believe in evolution if you tell them what the professors believe -- that life in all its complexity assembled itself as a result of a series of lucky hits; that we live in a world of random changes that sometimes "coincide" with the environment (natural selection); and that's how we got here.

To believe that, we first have to be blinded by antagonism to the normal, automatic recognition of purpose and design in nature. And for most people, this blindness has to be inculcated; by teachers, by the academy, by the culture.

As to the possibility of our reaching the professor group, the trouble with my correspondent's design versus "accidental mutation/natural selection" formula is not that it is too wordy but that the professoriate have learned to accept that accidental mutation and natural selection can explain everything under the sun.

I have often wondered: What would it take for a biology professor to see some living organism, study it and then clap his hand to his forehead and say: "Wow, natural selection couldn't possibly have done THAT!"

Answer: Nothing. They are locked into a materialist worldview, and they think that anything outside it is unscientific. They have already accepted Lewontin's Law about the necessity of a "prior commitment to materialism." They will look at any strange organism you may show them and say: "Well, it exists doesn't it? How else did it get here, if not by gradual stages, bit by bit, starting with molecules in motion, finally building up to what we see in front of us? What other choice is there?"

In such a dogmatic environment dissenters wisely keep their mouths shut and upholders of the orthodoxy firmly close their minds.

Of course they don't like it when we refer to them as IDiots or creationists but they have an answer to that one as well.

Going beyond that, some of our better-known adversaries indulge in name-calling so mechanically that they may well have ceased to understand the issues. It's as though they become unable to think about what they don't want to think about. Those who resort to slogans like "ID creationism" often show no sign of understanding what the claims of ID are, sufficiently even to be able to restate them.

Unfortunatly for the IDiots, I actually understand the issues better than they do! Here's the main tenets of Intelligent Design Creationism.

1. Darwin is evil and gave rise to Hilter. Evolutionists are wedded to atheism and materialism. Most scientists are too stupid to interpret evidence correctly. Evolution cannot account for life as we know it.
2. Life can only be explained by invoking an Intelligent Designer but we're not going to tell you how or when he/she/it did it.
3. The Intelligent Designer is not necessarily a god. We never said that so you can't accuse us of being creationists.
4. The general public is being prevented from learning the truth about creationism anti-evolutionary theory by a vast conspiracy of dogmatic scientists who control higher education (and almost everything else in some secular "foreign" countries like France or Japan).

Do you think I got it right?

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Does Environmental Change Drive Evolution?

I recently posted an article on the lack of evolution in species that have lived through several ice ages {More Evidence of Short-term Stasis]. This prompted a discussion about whether any serious evolutionary biologists really believe the opening statement in the abstract of the paper, "Conventional neo-Darwinian theory views organisms as infinitely sensitive and responsive to their environments, and considers them able to readily change size or shape when they adapt to selective pressures" (Prothero et al. 2012).

I believe that lots of biologists think like this. Let's discuss a quotation from The Blind Watchmaker (1986, p.178-179) by Richard Dawkins. How many readers agree with him?

After many generations of cumulative selection in a particular place, the local animals and plants become well fitted to the conditions, for instance weather conditions, in that place. If it is cold the animals come to have thick coats of hair, or feathers. If it is dry they evolve leathery or waxy waterproof skins to conserve what little water there is. The adaptations to local conditions affect every part of the body, its shape and color, its internal organs, its behavior, and the chemistry of its cells.

If the conditions in which a lineage of animals lives remain constant; say it is dry and hot and has been so without a break for 100 generations, evolution in that lineage is likely to come to a halt, at least as far as adaptations to temperatures and humidity are concerned. The animals will become as well fitted as they can be to local conditions. This doesn't mean that they couldn't be completely redesigned to be even better. It does mean that they can't improve themselves by any small (and therefore likely) evolutionary step: none of their immediate neighbors in the local equivalents of 'biomorph space' would do any better.

Evolution will come to a standstill until something in the conditions changes: the onset of an ice age, a change in the average rainfall of the area, a shift in the prevailing wind. Such changes do happen when we are dealing with a timescale as long as the evolutionary one. As a consequence, evolution normally does not come to a halt, but constantly 'tracks' changing environment. If there is a steady downward drift in the average temperatures in the area, a drift that persists over centuries, successive generations of animals will be propelled by a steady selection 'pressure' in the direction, say, of growing longer coats of hair. If, after a few thousand years of reduced temperature the trend reverses and average temperatures creep up again, the animals will come under the influence of the new selection pressure, and will be pushed towards growing shorter coats again.

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Prothero, D.R., Syverson, V.J., Raymond, K.R., Madan, M., Molina, M., Fragomeni, A., DeSantis, S., Sutyagina, A., and Gage, G.L. (2012) Size and shape stasis in late Pleistocene mammals and birds from Rancho La Brea during the Last Glacial–Interglacial cycle. Quaternary Science Reviews 56:1–10. [doi: 10.1016/j.quascirev.2012.08.015]

More Evidence of Short-term Stasis

A group of paleontologists recently documented stasis in birds and mammals from 35,000 years ago to today (Prothero et al., 2012).

Intelligent Design Creationists such as Douglas Axe are surprised by this result [Tar Pit Study Shows Complete Absence of Evolutionary Change]. So, apparently, are the authors even though they are evolutionary biologists and they have published this observation before.

How many Sandwalk readers are surprised by this paper?

Understanding Evolution in New England Colleges and Universities

The March issue of Evolution: Education & Outreach contains an interesting article on "Educators of Prospective Teachers Hesitate to Embrace Evolution Due to Deficient Understanding of Science/Evolution and High Religiosity" (Paz-y-Miño-C and Espinosa, 2012). The authors surveyed three groups at 17 colleges and universities in Maine, New Hampshire, Vermont, Massachusetts, Connecticut, and Rhode Island in the USA (New England states). The three groups were (1) general faculty members, (2) faculty members who were involved with training prospective teachers (educators), and (3) undergraduates.

Most of the general faculty (82%) thought that evolution was definitely true but only 54% of the students agreed. Among the educators only 71% thought that evolution was definitely true. This is a general trend. Educators tend to be more religious and less certain of evolution than typical faculty members but less religious and more accepting of evolution than the average student.

Why Are Chimps Still Chimps?

The American Biology Teacher published an issue dedicated to evolution back in February 2012. I got a chance to see this issue when I was in Ottawa for a big evolution meeting last July but it's taken me this long to blog about it.

One of the most impressive articles is Why Are Chimps Still Chimps" (Johnson et al. 2012). It answers the most common questions from students about human evolution and the evolution of our closest cousin, the chimpanzee.

You will learn about the difference between anagenesis and cladogenesis and why our common ancestor might have looked more like a modern chimpanzee than a modern human.

Johnson et al. are addressing teachers and they know it's important to directly refute students' misconceptions in class. They do a good job of pointing out those misconceptions.

Here's the conclusion of their paper.

If humans evolved from chimps, why are there still chimps? The two major misconceptions this question reflects are that evolution is (1) always linear and (2) innately progressive. The common depiction of evolution as a linear progression throughout which ape-like creatures become more like modern humans is a gross simplification (see Gould, 1989, for further discussion of the iconography). Along these lines, we encourage educators to find images of human and ape family trees in which the human–chimp common ancestor is depicted as an illustration, rather than those that use photographs of chimps to represent this common ancestor – reinforcing the very misconception we are trying to avoid. As we discussed, much of evolution results in a pattern known as cladogenesis; this involves processes that have given rise to the tree-like pattern of the diversity of life. Moreover, evolution does not necessarily equate to progress, as change is not always progressive (Ruse, 1996). It is incorrect to speak of living organisms as more (or less) evolved than other living organisms. Chimps are just as evolved as humans. The lineages leading to chimps and humans split from one another some 6 million years ago; since then, each has taken its own path.

This is an example of the misconception that we need to refute ...

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Johnson, N.A., Smith, J.J., Pobiner, B. and Schrein, C. (2012) Why Are Chimps Still Chimps? The American Biology Teacher 74:74-80. [DOI: 10.1525/abt.2012.74.2.3]

Monday's Molecule #190

Last week's molecule was carnitine (3-hydroxy-4-(trimethylazaniumyl)butanoate) or carnitine. The winner was Raúl Mancera [Monday's Molecule #189].

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

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.)

Eschaton 2012 Is Coming!

THE WORLD IS PROBABLY NOT ENDING.
NOW STOP WORRYING, AND CELEBRATE REASON!
Come to Ottawa for a weekend gathering of scientists, philosophers, authors, academics, skeptics, rationalists, humanists, atheists, and freethinkers, where you can see presentations and join discussions on science, skepticism, gender issues, theocracy vs secularism, godless ethics, parenting beyond belief. Featured speakers include blogger PZ Myers, author Ophelia Benson, philosopher Chris DiCarlo, science education activist Eugenie Scott, and many others. You can even participate in a live recording of Canada's skeptical podcast, "The Reality Check" (trcpodcast.com).

Saturday evening we present our gala "Night at the Musuem" (held at the Canadian Museum of Nature), which includes a reception, talk by PZ Myers, and late night special events, with exclusive access to the Fossil Gallery and Earth Gallery.

The price of $275 ($225 for CFI members) includes access to the Friday night plenary session, a choice of 2 daytime tracks on Saturday and Sunday, lunches and snacks, plus the Saturday evening gala. (A limited number of volunteer discounts are available - email volunteers@eschaton2012.ca for more information.)

Eschaton 2012
November 30-December 2
Ottawa, Canada

The best event, by far, will be Saturday morning ...

9 AM: Eugenie Scott
10AM: Larry Moran "Science vs IDiots"
11AM: PZ Myers
11:30 AM: Audience Q+A, panel on science education (PZ Myers, Eugenie Scott, Larry Moran)

See you there!

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A Dishonest Intelligent Design Proponent?

Most IDiots are ignorant about evolution and they let their religious biases interfere with the proper interpretation of scientific data. We excuse their mistakes on the grounds that they don't know any better.

However, some IDiots clearly should know better. They have advanced degrees in relevant fields and they have received considerable feedback on the claims they post or the books they write. We know they have read the critiques so when they persist in repeating falsehoods, there must be another explanation. They must be lying.

Jonathan Wells has a Ph.D. in molecular biology. He has posted numerous articles about junk DNA and he was written a book on the subject (The Myth of Junk DNA). Lots of people have made comments about his blog posts and his book has been widely critiqued. Many of his claims have been shown to be false.

So what do we make of his recent post on Evolution News & Views) (sic) entitled Why All the Fuss Over Some Junk?. We are forced to conclude that Wells is dishonest. Perhaps with the caveat expressed by Peter Medawar many years ago in his review of Père Teihard's The Phenomenon of Man.

Yet the greatest part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that he has taken great pains to deceive himself.