Andyjones has responded to my post on failing to educate him about science. His response is: Failure to Educate? Failure to Persuade. I'm reposting his entire response ....
Larry Moran replied to my latest post with an admission of failure. He thinks he has failed to educate, but I think rather he is confusing the word ‘persuade’ with the word ‘educate’.
He thinks I am rationalising junk DNA with a pile of ‘what-ifs’. But the fact is that most of my ‘what-ifs’ are already known to have some basis in reality. I am not denying any obvious reality. Indeed, the basic machinery of life looks like design, far more than when Paley was around. Yes, there could also be a great deal of junk. That’s why I have said a number of times that ID is not committed to the idea that there is no junk.
Yet, from my point of view, I see a whole pile of Darwinian/post-Darwinian materialists who have only partly explored the genome, working from an assumption that the genome was not designed, and thus are jumping the gun on the evidence. For example, Larry still seems to think that pseudogenes are of themselves ‘solid evidence’ of broken genes despite the fact that we know that at least some pseudogenes influence the rate of translation of real genes by competing with them; a simple design reason why there should be ‘false genes’ = pseudogenes. Who has explored the rest of them?
From his emotive response to my perfectly valid, albeit speculative suggestions (though they were not plucked out of the air either), I don’t trust this guy to think clearly and calmly about the possibility of design. That’s the real problem.
This is all very frustrating. Why do IDiots who have no serious training in biochemistry and molecular biology think they know more than the experts?
And why do they refuse to learn when we attempt to educate them?
Do you remember when Stephen A. Batzer listed several reason why "Darwinists" are so uncivil? [Why Darwinism and Incivility Seem to Go Together] I blogged about it at: Why Are "Darwinists" So Uncivil?. We all had a good chuckle about hypocrisy and stupidity.
You've also seen many IDiots defend their use of "Darwinism" by claiming that it's nothing more than an accurate description of the most important scientific prerspective on evolution.
Here's what David Klinghoffer wrote today in Scientific Anti-Humanism Is Being Refuted by Science Itself.
Scientific anti-humanism refers to the cheapening of human dignity and of the value of human life in the name of science. Among many other pieces of novel information on that theme, the most important point that came out of Michael Medved's discussion with John West just now on the Science and Culture Update is that this corrosive tendency is being refuted by science itself.
Darwin persuasively taught that life is the product of blind, meaningless, purposeless churning, making all life, not just human, hardly anything more special or dignified than cosmic refuse. Indeed in a Darwinian worldview, life is cosmic refuse. While accused abortion butcher Kermit Gosnell may be an outlier, he is an emblematic personality in our Darwin-tutored culture.
How civil of him to link Darwinism with Kermit Gosnell.
Remember, this is Evolution News & Views (sic), sponsored by the Discovery Institute. This is not some backwoods hack operating on his own. It's mainstream civility for the leading Intelligent Design Creationists.
UPDATE Klinghoffer posted the following a short time later in Darwinism Versus Reality: The Painful Divorce. It's just another example of how the IDiots link "Darwinism" with immorality and it puts the lie to the claim that "Darwinism" is just another word for "evolutionary biology."
I wanted to highlight what Josh Youngkin said yesterday in his very perceptive comments about the Jodi Arias verdict. Darwinian materialists like Jerry Coyne end up asserting there's no free will, therefore no such thing as moral responsibility. A murderer may be locked up for everyone else's safety, but not because we're correct to seek to impose retribution. We have no moral right to do so.
As Josh says, this casts the human being who murders as a fundamentally blameless animal, like a man-eating tiger. We would cage or even shoot such a tiger, but we could not blame it for acting as it does.
Profoundly, I thought, Josh's article suggests how remote from human experience a guy like Coyne must travel if he wants to carry his Darwinian materialism to its seemingly logical conclusions.
The results of the 2011 Canadian census are beginning to appear. Indi at Canadian Atheist has prepared a nifty pie chart showing that 63.7% of the population identifies themselves as Christians [2011 National Household Survey religion results].
In second place, at 23.9%, are those who say they have no religion. We know that many of the "nones" will not call themselves "atheists" but they might as well be.
The take-home lesson is that almost 24% of Canadians are not religious. That's up from 16.5% in 2001. Times they are a -changin.
The question on the census was ...
22. What is this person’s religion?
Indicate a specific denomination or religion even if this person is
not currently a practising member of that group.
For example, Roman Catholic, Ukrainian Catholic, United Church,
Anglican, Lutheran, Baptist, Greek Orthodox, Jewish, Islam, Buddhist,
Hindu, Sikh, etc.
Specify one denomination or religion only __________
No religion __________
I think you can see why nonbelievers may be somewhat higher than the numbers indicate.
A few weeks ago I decided to give Intelligent Design Creationist andyjones the benefit of the doubt and assumed that he really wanted to understand enough biology to have a credible opinion about genomes and junk DNA. I published a series of posts on Educating an Intelligent Design Creationist: Introduction.
Andyjones has replied to my post with: Getting me an Education.
My first post was: Educating an Intelligent Design Creationist: Pervasive Transcription. I refuted the misconception that nobody ever investigated pervasive transcription and I explained that we know a great deal about the parts of the genome that are being transcribed, and why they are transcribed. I did not claim that this was solid evidence for junk DNA. That wasn't the point. The point was to teach andyjones that there are explanations for pervasive transcription—we don't call it junk just because we have no idea what's going on.
I also pointed out that using pervasive transcription as an argument for function (i.e. against junk) doesn't really cut it unless you don't understand basic biochemistry. Here's how andyjones responded ...
Larry thinks this (especially the situation from the 80s on) amounts to solid evidence for junk DNA, but I honestly don’t see how it does.
Okay. So my attempt to explain the reality of the situation failed miserably.
The Intelligent Design Creationists, otherwise known as IDiots, are getting desperate. They have been relentlessly promoting Stephen Meyer's upcoming book Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design but so far they have pretty much failed to trick evolutionary biologists into trashing the book before it's published.1 That must be a major disappointment to them.
The baiting continues with an article by David Klinghoffer on the Evolution News & Views (sic) site: What Darwin's Enforcers Will Say About Darwin's Doubt: A Prediction. Here's what he predicts ....
Among possible lines of attack against Stephen Meyer's forthcoming book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, I foresee some critics trying to argue that it's not fair game for Dr. Meyer to invite the general reading public to consider what's going on in peer-reviewed technical literature pertaining to evolution.
After all, biologists should have the opportunity to air their views in a semi-private professional setting without "creationists" barging in and telling the unwashed masses that many scientists have already given up on the Darwinian paradigm and are seeking post-Darwinian alternatives. Even though it's true, still it's wrong to publicize the fact, thereby leading the common folk astray and confirming their prejudice in favor of seeing life and the universe as reflecting some purpose.
This time I will rise to the bait if only for the purpose of preserving this prediction so we can revisit it in the future.
I'd also like to note, for the record, that the IDiots have published a number of books in the past and I don't recall anyone making the argument that Klinghoffer predicts. Can anyone out there point me to an article where scientists criticized the IDiots for pulicizing controversy within the evolutionary biology literature? It would be quite hypocritical for most bloggers to do so since criticizing the scientific literature is what we do.
Is it just my imagination or have evolutionary biologists also published books where they "expose" the controversies within evolution. If scientists do it routinely then why in the world would they criticize an IDiot for doing it? That doesn't make any sense, does it? (Oops, I inadvertently made the false assumption that IDiots are supposed to be rational.)
Finally, Udo Schüklenk alerted me to this creationist article because he is mentioned. Klinghoffer refers to a discussion about the ethics of infanticide and he thinks that his creationist2 buddy Wesley Smith is being attacked for exposing a debate within the bioethics community. You should read the papers he links to along with Udo Schüklenk's paper [In defence of academic freedom: bioethics journals under siege] if you want to catch up on that discussion. As usual, the IDiots get it all wrong. Are you surprised?
1. That's mostly because we don't care. We are not anticipating anything we haven't heard many times before although, I suppose, we could be surprised.
2. Smith is a lawyer and a Senior Fellow at the Discovery Institute. I don't know what kind of creationist he is.
The last Monday's Molecule was α-linolenate [Monday's Molecule #203]. It is an omega-3 essential fatty acid. The winner was Anders Ehrnberg.
Today's molecule is actually three different molecules (1,2 and 3). Give the common names for the terminal part of each molecule—the names used in most textbooks. Identify E2 (enzyme name) and briefly explain what's going on.
Email your answers to me at: Monday's Molecule #204. I'll hold off posting your answers 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 email message.)
The Centre for Inquiry logo (above) is from the CFI Canada Facebook page. It's an amazing piece of work because it embodies one of the key features of CFI as an umbrella organization that brings together a number of different groups to unite around common goals.
This is a lot harder than you might think. I think of myself as a skeptic and an atheist but I am not a Humanist. If an organization like CFI were to be taken over by Humanists, I could not be a member. Other people are worried that CFI might be dominated by atheists and an atheist agenda. Some of them have left the organization because they think of themselves as skeptics who are not anti-religion.
Lately the conflict between (some) skeptics and atheists has claimed another victim. PZ Myers is so upset with the narrow view of skepticism promoted by Jamy Ian Swiss [see Skeptics have the amazing superpower of being simultaneously fierce and timid] that he now declares, "I officially divorce myself from the skeptic movement."
What's the problem? It's that some skeptic movements want to concentrate on pseduoscience and pseudomedicine and leave religion alone. They are atheists and accommodationists. Not content with just ignoring vocal atheists, they criticize their tactics as being offensive and inimical to the important skeptical causes. I don't agree with that version of skepticism and neither does PZ Myers. However, unlike PZ, I think the solution is to make it clear that people like Jamy Ian Swiss are wrong to exclude atheism from the skeptical movement.
If the skeptical movement becomes officially accommodationist and anti-atheist then I will have to abandon it just like PZ Myers did.
The advantage of CFI is that it can "accommodate" all these points of view, if we are careful. It can promote an "Extraordinary Claims" campaign that links skepticism about religion and skepticism about pseudoscience and quackery. It can launch a campaign against religion in the schools without antagonizing believers. It can promote charitable causes that bring together freethinkers, humanists, and atheists. It can sponsor Humanist officiants who can preside at weddings and funerals. It can do much to promote what all those groups have in common. All we have to do is tolerate the occasional cause that we might not completely agree with.
It's a bit ironic that PZ Myers is offended by the direction that skepticism is taking yet seems blind to the re-branding of "freethought" that he supports. I'm hoping that in Canada we can avoid the competing conferences that pit freethoughters against skeptics and atheists against humanists. So far, we seem to be on the right track with the Committee for Advancement of Scientific Skepticism (CASS) and CFI events celebrating Dawkins & Krauss and "The Unbelievers" as well as Eschaton 2012, and the upcoming Imagine No Religion.
UPDATE: Jack Scanlan of Young Australian Skeptics says, "A person can be a skeptic and believe in a god." [PZ’s Problem: Does Skepticism Makes An Exemption For Religion?]. I disagree.
Let's ignore for a minute the people who comment on Sandwalk because it's clear that the most uncivil group is the creationists. Let's also ignore the people who comment on the creationist blogs because there it's also the supporters of religion who are the most uncivil. Oh hell, let's just ignore reality altogether and assume, for the sake of argument, that supporters of evolution are more uncivil than creationists.
Stephen A. Batzer speculates, very civilly, why this imaginary assumption might be true [Why Darwinism and Incivility Seem to Go Together].
- They're human. That says a lot that's negative about them and of course about us, too.
- They're typing, probably anonymously, on the Internet. I'm sure you have noticed the level of discourse on the Internet. The Lincoln-Douglas debates it isn't. On any topic.
- You are challenging their religious beliefs, which they know, just know, to be true.
- Thought leaders in the Darwinian movement, such as Dawkins, Prothero, Shermer and so on, inculcate and advocate incivility by their own example. Look at the way biologist James Shapiro and philosopher Jerry Fodor have been treated. It's ugly.
- "A little knowledge is a dangerous thing." That Darwinism is a FACT has been proclaimed since before all of us were born. Saying that the Darwinian mechanism of speciation is not a fact strikes many folks as if you're intimating that there is no Japan. It's just a made up country. When I try to measure the level of personal knowledge that Internet advocates have of evolutionary theory, it is almost universally superficial. This includes biologists.
- They have not taken the time to understand what the issues are or what evidence is convincing to those who disagree with them. They are ignorant in a nearly comprehensive way about why thoughtful, educated people find the "generate and filter" paradigm causally insufficient.
Isn't that amusing?
Now for the next bit ...
WARNING!!! Turn off your irony meter. It doesn't matter whether you have the updated Mark VIII with the extra power pack or not. Turn it off, NOW!!!
Here's how Stephen A. Batzer ends his post on Evolution News & Views (sic).
One thing that draws me to the ID movement is that it has the polite and understated ethic that science is supposed to have -- but does not have when the subject is evolution.
This month's Carnival of Evolution is hosted by Dirk Steinke at DNA Barcoding. He's another one of those nasty Canadian bloggers who seem to be everywhere these days. Read: Carnival of Evolution #59: A letter from the Doctor
Dear Wilfred,
Are you still watching the stars with your new telescope? I bet you can see what I see outside the windows of my TARDIS. The star you're searching for is still there, it just tends to fall out of view occasionally.
Do you remember how you always said how you'd love to be travelling with me again through the skies? I envy you right now, living on this wonderful planet in your lovely little house treating yourself to a flask of tea on your porch while you look at the stars. They're beautiful, I would know, I live amongst them and I've traveled to so many. I’ve seen galaxies born and fading away.
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.
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Steven Novella blogs at Science-Based Medicine. Yesterday he was upset about American politicians who want to restrict research grants to projects that "advance the national health, prosperity, or welfare, and to secure the national defense" [Politics of Public Research Funding]. The goal is to put a stop to silly basic science research like studying sex in snails.
Here's the quote of the day from Steven Novella.
I have noticed, however, that researchers have become reflexively good at making up plausible-sounding possible applications for their basic science research – as if they have to constantly justify their research. Every basic-science study that looks at viruses, therefore, may one day cure the common cold. Anything dealing with cell replication may be a cure for cancer. Any materials advance will lead to supercomputers or superlight vehicles. All brain research, apparently, might one day cure Alzheimer’s disease.
I would love for a scientist to say something to the effect of “I have no idea what, if any, practical use this research might lead to, but the knowledge is really cool”. I guess you just don’t say that to a grant committee, however.
The students in my Molecular Evolution course have written the final exam. I finished grading the exams yesterday and the final course marks have been submitted. Now I don't have to think about teaching until August.
Just for fun, I'm posting the final exam questions. How do you think you'd do? I gave the students a list of all possible questions on the last day of class. The only one they hadn't seen was question #2. They knew that the first question would definitely be on the exam.
Students had to answer questions 1 & 2 and choose any three of the other questions.
- Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.
- Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2013. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 109 bp.)
- There are hardly any pseudogenes in bacterial genomes. Why haven’t pseudogenes been eliminated from our genome?
- Explain the two-fold cost of sex. Why is this a problem in evolutionary theory?
- Richard Lenski’s group at Michigan State University has been following the evolution of 12 cultures of E. coli for over 50,000 generations. All 12 cultures are grown under exactly the same experimental conditions and the mutation rate is high enough that every culture has been exposed to multiple mutations at every base pair in the genome. Explain why only one of the cultures has evolved the ability to use citrate as a carbon source.
- Why is the Three Domain Hypothesis being challenged by some molecular evolutionary biologists? What are the alternatives?
- What do you think of Kirschner and Gerhart’s “Theory of Facilitated Variation.” Is this something that has to be incorporated into a new extended version of evolutionary theory? What, if any, are the limitations of the theory and what, if any, new insights into evolution does it provide?
Most of you think of Richard Dawkins as a "strident atheist" who doesn't suffer fools gladly.1 The first part of that reputation ("strident atheist") is unjust as Dawkins pointed out on several occasions when he was in Toronto earlier this week.
The second part ("doesn't suffer fools gladly") is quite true. Dawkins thinks that foolish things, like religion and other superstitions, deserve to be ridiculed.
Richard Dawkins and I agree on atheism but disagree on some aspects of evolution. I'm pleased to report that he didn't hold that against me when we met for brunch a few days ago. I guess that means I'm not a fool in his mind! 
For those of you who have never had the pleasure of meeting him, I want to assure you that in person he is a very pleasant fellow and lives up to the very British expression, "a scholar and a gentleman."
Some of the people I met were wondering about the reasons why I disagree with some aspects of Richard's views on evolution. They haven't heard of Stephen Jay Gould and I find that very sad. I still believe that everyone interested in evolution has to read and understand the "Spandrels" paper.
Here's a short reading list ....
Michael Lynch on Adaptationism
What Does San Marco Basilica Have to do with Evolution?
Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift
1. The phrase comes from the New Testament [Suffer fools gladly].
The last Monday's Molecule was medium chain acyl-CoA dehydrogenase (MCAD) (PDB 2AIT). Nobody got the right answer [Monday's Molecule #202].
Today's molecule is very important for humans. You need to supply the common name AND a more official IUPAC name that identifies the configuration of the bonds. You also need to briefly explain why this molecule is important in humans.
Email your answers to me at: Monday's Molecule #202. I'll hold off posting your answers 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 email message.)
Here's a CNN interview with Richard Dawkins and Lawrence Krauss. It was recorded this morning. It's very unfortunate that the reporter (Poppy Harlow) injects her own views on religion but at least they serve to illustrate the prejudice against unbelievers.
There are quite a few CNN reporters who broadcast their Christian views at every opportunity. They just don't get it.
Today is my daughter's birthday. She was born quite a few years ago in Geneva Switzerland while I was a postdoc.
Here's Jane with my grandchildren, Zoë and Luca (right). Below is Luca studying gamma ray bursts at the Griffiths Observatory in Los Angeles. Gamma ray bursts were the subject of Jane's Ph.D. thesis.
