Friday, November 23, 2012

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.


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

Thursday, November 22, 2012

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.


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!


Wednesday, November 21, 2012

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



Tuesday, November 20, 2012

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.


[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.


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


Monday, November 19, 2012

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.)

Sunday, November 18, 2012

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.



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.



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?


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."


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

Thursday, November 15, 2012

Wednesday, November 14, 2012

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!


Monday, November 12, 2012

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.


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?


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.


The lectures are sponsored by The Copernicus Group.
The Copernicus Group is based in Toronto, Canada. The group provides lectures in the Greater Toronto Area on Science and Faith issues particularly in Origins Science – that is: the origin of the universe, life, species and related subjects.

The Copernicus Group derives its name from Nicholas Copernicus the Polish astronomer who in 1543 published his finding that the earth revolved around the sun. His discovery was not readily accepted because the view held by most educated people of the day was that the sun revolved around the earth. The conventional view was wrong because the foundational assumption regarding the universe – that the earth and human life must be at its center – was wrong. Today science has a very similar foundational assumption – all processes must be understandable to humans by naturalistic processes.

Foundational assumptions affect conclusions. As a result The Copernicus Lectures on Science & Faith will attempt to present scientific observations in a neutral manner – meaning that neither the Naturalistic assumption nor any religious assumption will be made as a starting point – and conclusions will be left to the audience members.


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.



Saturday, November 10, 2012

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?

Wednesday, November 07, 2012

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.



Thursday, November 01, 2012

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).