A New View of Evolution

There have been lots of new books about evolution in the past decade or so. I tend to divide them into three categories:

1. The Standard View: These are books that basically support the Modern Synthesis with some small tweaks here and there. They do not advocate major shifts in the way we look at evolution. Books by Richard Dawkins (The Greatest Show on Earth: The Evidence for Evolution), Jerry Coyne (Why Evolution Is True), Sean B. Carroll (Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution), and Ken Miller (Only a Theory) fall into this category.
2. The New View: Some books make the case for a new way of looking at evolution. I'll call it the "New View." Many of Stephen Jay Gould's books fall into this category (The Structure of Evolutionary Theory). He refers to it as extending the modern synthesis. Most of the "extension" is based on a pluralist, rather than an adaptationist approach but other modifications are important. Two recent books by Michael Lynch (Origins of Genome Architecture) and Eugene Koonin (The Logic of Chance: The Nature and Origin of Biological Evolution) fall into this category. It's a view that I share.
3. The Radical View: Some books advocate a more-or-less complete overthrow of the Modern Synthesis, replacing it with the author's pet theory. Examples are: Marc Kirschner, and John Gerhart (The Plausibility of Life: Resolving Darwin's Dilemma), James Shapiro (Evolution: A View from the 21st Century), Lynn Margulis and Dorion Sagan (Acquiring Genomes: A Theory Of the Origin Of Species), Massimo Pigliucci and Gerd B. Müllerand (editors) (Evolution - the Extended Synthesis), many others.

The Problem with STEM

The new buzzword in science education is STEM: science, technology, engineering, and math. In America, there are dozens of studies on how to improve STEM education at all levels—including universities. Leading scientists have signed on.

Here's the problem. "Science" is NOT the same as "technology" and not the same as "engineering." There's a big difference between learning science and learning how to build things. The purpose of a degree in technology and engineering is obvious—it's job training. The purpose of a science education is quite different—it's supposed to teach you how to think critically.

But that distinction seems to have been lost on politicians, the general public, the media, and—most disappointingly—my fellow scientists. A recent article in The New York Times illustrates the extent of the problem [Why Science Majors Change Their Minds].

The New Scientific Version of Intelligent Design Is Compatible with Junk DNA

 

Over on Uncommon Descent we've been discussing junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. One of the IDiots (Joseph) has proposed a modification of the existing scientific theory of intelligent design. The new version now accounts for junk DNA.

You might think this is just his personal take on intelligent design but I asked everyone else to comment if they objected to his ideas. After more than 24 hours, nobody raised any objection so I assume Joseph's ideas are acceptable to the other IDiots.

The new version goes like this .....

1. You can have junk DNA because physical constraints and design compromises prevented a perfect design.
2. Due to genetic entropy the originally designed genomes might have degenerated.
3. Junk DNA could have been put in the genome by the intelligent designer as preparation for future creations.
4. Some of the junk DNA is redundant functional DNA that's present in case a gene breaks down.

This new version of intelligent design is not in conflict with the presence of large amounts of junk in our genome.

The evolution side should know about this new development just in case we're ever accused of not keeping up with the latest advances in Intelligent Design Creationism.

UPDATE: Some readers are a little confused by this article. Of course there's no "new" version of Intelligent Design Creationism. Joseph's speculations are completely at odds with the views of the leading IDiots like Dembski, Myers, Wells, Behe etc. Most of the "leading lights" think there's a serious problem with junk DNA. According to them, ID predicts that most of our genome will be functional.

The point of my article is that the IDiots never criticize or correct their friends no matter how stupid they get. That's why you won't see any proponents of intelligent design posting comments below that question Joseph's statements.

BTW, Joseph, or Joe G, is a field service engineer. Please refrain from making unflattering comments about The Salem Conjecture. (That's my job.)

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The Wreck of the Edmund Fitgerald

 
Twenty-nine men died on November 10, 1975 when the S.S. Edmund Fitgerald sank in a storm on Lake Superior.

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Ahem!

 
David Klinghoffer is at it again: How Ignorance Insulates the New Atheists

First, that's because the key argument against belief in God lies, as it always did, in the attempted critique of the design argument. New Atheists like Richard Dawkins recognize this, and so does Coyne. Otherwise why would he name his blog, a venue overwhelmingly devoted to religion bashing, "Why Evolution Is True"? Yet the New Atheists have uniformly kept themselves just as ignorant of modern expressions of the design argument as they have of adult religious beliefs. When Dawkins goes after Darwin-doubters, he ignores -- will not debate, will not grapple with in print, probably doesn't even read -- proponents of intelligent design, a credible scientific alternative to and critique of Darwinian evolution. So too with Coyne. When Dawkins or PZ Myers or the rest does critique a Darwin doubter, it's always some hapless creationist, apprehended unarmed in the Internet wasteland and presenting a nice easy target. Like a schoolyard bully, they will pick on the little kids, but never on an opponent their own size.

Aside from David Kinghoffer, I don't usually pick on hapless creationists. I'm more than happy to pick on the very best that Intelligent Design Creationism has to offer. Problem is, they don't listen to me.

Is that because the IDiots prefer to attack the small fry rather than stand up to someone their own size (or larger)?

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Carl Sagan Day

 

Happy Carl Sagan Day.

In every such society there is a cherished world of myth and metaphor which co-exists with the workaday world. Efforts to reconcile the two are made, and any rough edges at the joints are tend to be off-limits and ignored. We compartmentalize. Some scientists do this too, effortlessly stepping between the skeptical world of science and the credulous world of belief without skipping a beat. Of course, the greater the mismatch between these two worlds, the more difficult it is to be comfortable, with untroubled conscience, with both.

In a life short and uncertain, it seems heartless to do anything that might deprive people of the consolation of faith when science cannot remedy their anguish. Those who cannot bear the burden of science are free to ignore its precepts. But we cannot have science in bits and pieces, applying it where we feel safe and ignoring it where we feel threatened—again, because we are not wise enough to do so. Except by sealing the brain off into separate compartments, how is it possible to fly in airplanes, listen to the radio or take antibiotics while holding that the Earth is around 10,000 years old or that all Sagittarians are gregarious and affable?

Carl Sagan, The Demon-Haunted World (1995) P. 297.

Visit Bad Astronomy: On the birthday of Carl Sagan to hear Carl Sagan read his famous essay "The Pale Blue Dot."

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I would so go to this if I were in Madison

 
Upcoming lecture in Madison¹

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1. Coincidentally, Ms Sandwalk and I were just talking—less than 15 minutes ago— about how long it would take to drive to Madison from Toronto. I think we could do it in 12 hours.

Haught vs Coyne: The Q&A

Here's an excellent summary of the Q&A from the debate. It's from Eric MacDonald at Choice in Dying: Q&A: Haught on God: Bitter, Impolite and Wrong.

He has a blow-by-blow account of the questions and answers following the debate but I especially like this ....

The assumption that science decided to leave out questions of god, meaning, purpose and value is a caricature of the history of science, and Haught, who claims to be making a serious attempt to show the compatibility of science and religion, must know this. If he doesn’t, and he really thinks that science made such a decision — how does “science” do this, by the way? — then his misunderstanding of the relation of science and religion is total.

When Haught turns around, then, and castigates Jerry by saying that everything that he said was a caricature, that every quotation that Jerry took from Haught’s work was taken out of context, and that instead of reading carefully and thoughtfully Jerry got his idea of god and theology from creationist websites, this was undoubtedly the most aggressive and impolite move of the whole debate. Listen to what he says:

Remember that John Haught is a Roman Catholic theologian. As far as I know he has never dissociated himself from the main teachings of the Roman Catholic Church. If he doesn't believe in any of the stuff that Jerry mentioned then isn't it up to him (Haught) to clarify what he does believe in?

Does he believe in the resurrection? Does he believe that humans have souls? Does he believe in miracles? Does he believe that God answers prayers? Does he believe the Nicene Creed? Are all these things compatible with science?

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How to Explain Creationism to People Who Don't Think Critically

 

Uncommon Descent isn't really the very best that Intelligent Design Creationism has to offer and Denyse O'Leary isn't in the same league as William Dembski and David Klinghoffer.

Nevertheless, from time to time Denyse comes up with a good example of IDiot thinking. A few days ago she asked the following question: How do you get ideas about design in nature across to people who are not learning critical thinking?.

That's easy. You write books like The Myth of Junk DNA, The Edge of Evolution, and Signature in the Cell. Non-critical-thinkers just love that sort of stuff.

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Two Kinds of Atheists

 

Let me remind you that Evolution News & Views is the Discovery Institute website. When it comes to defending Intelligent Design Creationism, this is as good as it gets.

Let me also remind you that David Klinghoffer is a Senior Fellow at the Discovery Institute. When you see an article by a Senior Fellow on the Discovery Institute website, you just know it's got to be good.

That's why I was so excited to see The Two Types of Atheists on Nov. 3, 2011.

I meant to say that broadly there are two types of people who call themselves atheists but only one really deserves the dignity of the term. The first category -- the peasant, clod, village atheist, am ha'aretz -- is the person like Jerry Coyne with a cartoon version in his head of some one religion or all religions. He rejects the cartoon, figuring that as far as faith goes in general, he's got it all figured out and it's all nonsense. This type of person typifies the New Atheist movement. He has very little of interest to say.

There's a second much rarer type, however, the person who has not only investigated at least one serious faith seriously but also experienced it, known believers, ideally was a believer himself at some adult stage of life. This person, in rejecting God, merits a real hearing.

Aren't you glad that you can get the best of the best by just reading David Klinghoffer on Evolution News & Views?

It amuses me to think of David Klinghoffer as an atheist in training.

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Professor or Hobo?

 

Can you tell the difference between a Professor and a hobo? Joseph Somody has posted a quiz. Check it out: Professor or Hobo?.

Joseph is the undergraduate winner of Monday's Molecule #147. I'll be having lunch with him on Wednesday. If you have any other pictures of professors or hobos, you could post a link in the comments and I'll be sure to pass them long. (Joseph will probably read them anyway.)

I'm thinking we could do a similar quiz for students—something along the lines of "university student or not?" There are plenty of pictures on facebook that professors could use.

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Monday's Molecule #148

 

Today, as a special treat, you get to identify three (3) different molecules. Give me the complete, unambiguous, names of these molecules to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

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.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

Name the molecules shown in the figure. Remember that your names have to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do. In this case there are trivial names for all of the molecules but make sure you have the stereochemistry correct.

New Rule: In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: Oh, oh. There's only one correct answer—congratulations Jason Oakley. I posted another answer that's almost correct (should be L-sorbose). All the rest of you need to review your understanding of Fischer projections. Here's a hint: Name This Molecule #1.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody

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Advice from Jonathan Wells on Junk DNA

 

Copied from Uncommon Descent (Denyse O'Leary): What advice, on junk DNA, would Jonathan Wells give Francis Collins or Richard Dawkins?.

From the Salvo Magazine interview with Jonathan Wells, by Casey Luskin. Wells is the author of The Myth of Junk DNA:

If you could have lunch with Francis Collins and Richard Dawkins, what would you say to them about their use of the “junk DNA” argument? [that there is no design in life]

Actually, Collins no longer relies on “junk DNA.” In 2007 he announced in an interview for Wired magazine that he had “stopped using the term.” In 2010 he wrote that “discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more ‘junk DNA,’ think again” (The Language of Life, pp. 5–6). Unfortunately, his followers at the BioLogos Institute (which he founded) seem to be unaware of this, because they continue to promote the myth that most of our DNA is junk. I would encourage Collins to set them right.

UD News does not think Collins would succeed. They are not Collins’s followers, they are Darwin’s men. They do not seek more knowledge than Darwin had. They seek to make what he knew part of the bedrock of Christianity.

Unlike Collins, Dawkins seems utterly oblivious to recent developments in genomics. I would encourage him to read some of the scientific literature.

Why? Dawkins can command international attention for not keeping up to date – because millions of tax burdens feel he speaks for them – and they don’t need to keep up to date either. Their champions are fronts for the dead orthodoxies that keep them in place.

Dear Jonathan Wells and Denyse O'Leary,

I have read The Myth of Junk DNA and I have read the scientific literature. What advice would you give me?

Why don't you respond to my review of The Myth of Junk DNA? What are you afraid of?

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Haught vs Coyne: The Letter

As most of you know, John Haught originally tried to prevent the release of the video of their debate. You can read the history on Jerry Coyne's blog: Theologian John Haught refuses to release video of our debate.¹

You might have missed John Haught's open letter buried in the comments (#122), so here it is. You can also read Jerry's reply. Read Coyne vs. Haught - advantage, Coyne for a third party perspective on whether Coyne's behavior was appropriate.

The facts are clear, as far as I'm concerned. The sophisticated Roman Catholic theologian chose to step into the fire pit of real debate and got badly burned. Now he's whining because the fire didn't play by his rules. Maybe he thought he would be protected just like Shadrach, Meshach, and Abednego?

Seriously, we all know what this is about. It's not about whether science and religion are compatible—they aren't. It's about giving religious views special privileges that we don't give to any other viewpoints. It's about the unwritten rule that we aren't supposed to criticize someone's personal faith.

For decades that unwritten rule has given carte blanche to religious leaders who can say whatever they want about scientists and atheists knowing that they won't be challenged to defend those views. That's changing in the 21st century. John Haught seems to have just discovered that his special privileges have been revoked.

He doesn't get out very much.

An open Letter to Jerry Coyne:

Dear Jerry,

Your distorted reading of my motivation for not releasing the video of our conversation in Kentucky has given birth to an inordinate number of hostile letters to me. Because of misleading statements on your website (11/1/2011), I have received a considerable amount of hate mail, often laced with obscenities, though often also tempered with inquisitive politeness. The mail mostly complains about my “cowardly” reneging on an alleged agreement that you falsely assume I made to post online the video of our panel at the University of Kentucky. When I was in Kentucky I was never asked to do so. Later, after reflecting on what to me was a most unfortunate event, I wrote to Prof Rabel requesting that any video not be released.

Anyway, Jerry, your own words impute cowardice to me for this refusal, but how do you know that’s the reason for my reluctance? Here is a typical reaction stirred up by your remarks: “What a pathetic, sociopathic dweeb you are. Hiding behind your sick belief system you call a religion. You are an insult to academia, and a dim bulb for the uninformed masses. You deserve the insults you are getting and should be fired. Coward, liar and fool you are, loser. And no doubt a Republican too!” (I’m tempted to say that I can live with every accusation except the last.)

I want to make it clear that Rob Rabel at the University of Kentucky has confirmed that I never gave permission before or after the panel to post the video. You need to make this clear to your audience. I never broke the agreement that you have unkindly caused your readers to assume I made.

However, the more interesting issue has to do with my reasons for refusing permission to post the video, and whether it was wrong for me to do so. I have no regrets about anything I had to say during the panel, and if you agree to post this letter on your site I will be happy to have the video released unedited, for public scrutiny. Those who are reading this blog are free to look at other videos of my comments on science and religion available online. They will see that I have no need to hide my views from the public, and in fact I am quite eager to have my thoughts made available provided they are presented accurately and fairly.

Why then do I hesitate in this case? It has to do with you alone, Jerry, not anyone else, including myself. I have had wonderful conversations with many scientific skeptics over the years, but my meeting with you was exceptionally dismaying and unproductive. I mentioned to you personally already that in my view, the discussion in Kentucky seldom rose to the level of a truly academic encounter. I agree that it was probably entertaining to the audience who gave us a standing ovation at the end. Nevertheless, instead of being flattered by this I went away terribly discouraged at what had just taken place. I wish to emphasize that I do not exempt myself from criticism.

The event at the University of Kentucky did not take place in the way I had expected. My understanding was that each speaker was to provide a curt 25-minute presentation of how he understood the relationship between science and theology. I did just this, and I have no objection to having that presentation made public. People who attended the event, moreover, can testify that in my presentation I avoided talking about or criticizing you personally. Instead I was content to make some very general remarks about why I consider science completely compatible with theology as I understand it.

When Robert Rabel of the Gaines Center at the University of Kentucky, a true gentleman who remains far above reproach in all of this, contacted me last summer and invited me to participate in the event, he asked me for names of people who would differ from my own position. I recommended you as someone who would definitely have a different perspective, to say the least. Prof. Rabel informed me that you agreed to participate with the qualification that you did not want to debate me, but simply to lay out your own way of looking at science and religion. I took this to mean that you would do something parallel to what I did in my presentation.

Instead, you used the event primarily to launch a sneering and condescending ad hominem. Rather than using your 25 minutes as an opportunity to develop constructively your own belief that science and religion are always and inevitably in conflict, you were content simply to ridicule rather than refute several of my own ideas, as you interpreted them. On the other hand, my own presentation, as those who watch the video will see, was a dispassionate attempt to have the audience understand some of the reasons why the new scientific picture of the universe is so troubling to many traditionally religious people. I don’t believe that at any point in that presentation I resorted to ridicule, or that I focused on, much less misrepresented, anything you have written. Instead, I argued in a purely academic way that scientism is simply unreasonable. This was clearly my main point, and I was expecting you to respond to it in an academic manner as well.

Rather than answering my point that scientism is logically incoherent–which is really the main issue–and instead of addressing my argument that the encounter with religious truth requires personal transformation, or for that matter instead of responding to any of the other points I made, you were content to use most of your time to ridicule several isolated quotes from my books. I was absolutely astounded by your woeful lack of insight into, or willingness to grapple with, the real meaning of these passages. Sophisticated argument requires as an essential condition that you have the good manners to understand before you criticize. Your approach, on the other hand was simply one of “caricature and then crush.” Citation of a few isolated sentences or paragraphs, the meaning of which requires reading and understanding many chapters, is hardly useful criticism. You grossly distorted every quotation you used, and then you coated over your [mis]understanding of these statements with your own uncritical creationist and literalist set of assumptions about the Bible and theology. There was no room for real conversation, as impartial viewers will notice.

Instead of trying to convince the audience of the logical coherence and philosophical finality of your belief that science is the only reliable guide to truth, you began by arbitrarily announcing to the audience that John Haught is the chief representative of theology in the conversation of science with religion. You gave no evidence for that, and in fact it is by no means evidently true. I am but one of a great number of theologians involved in the discussion, and many others do not share my views. But your strategy was to show that if the principal figure is stupid, then you need not take his subordinates seriously either. This is a convenient method for shrinking the territory that needs to be covered, but it is hardly a fair way of dealing with all the other theological alternatives to your own belief system.

But let me come to the main reason why I have been reluctant to give permission to release the video. It is not for anything that I said during our encounter, but for a reason that I have never witnessed in public academic discussion before.

I’m still in shock at how your presentation ended up. I was so offended both personally and as an academic by the vulgarity of it all that I did not want other people to have to share what I witnessed that night in October. I still don’t.

I’m referring to the fact that your whole presentation ended up with a monstrous, not to mention tasteless, non sequitur, to give it the kindest possible characterization. You put on the screen a list of all the “evils” you associate with Catholicism: its stance regarding divorce, contraception, priest pedophilia, homosexuality–and I can’t remember what all–as though these have anything at all to do with the topic of the panel or with my own personal views on the relationship of science to theology. The whole focus of your presentation was on me, but when you came to your conclusion you never bothered to find out what my own position regarding your list of Catholic evils might be. I have never witnessed such a blatant smear or malicious attempt to impute guilt by association in all my years in university life.

Your list of Catholic evils, contrary to what you were suggesting, has absolutely nothing logically to contribute to your argument that science is opposed to religion. But even if it did, you never asked me whether I dissent from some or all the items on your list of “evils,” as many Catholics do, and whether such dissent might, in your twisted way of arguing, perhaps make my own position more credible. Your insinuation could only have been that somehow the priest sexual abuse crisis, for example, discredits my views on science and theology. You should be grateful that I have tried to protect the public from such a preposterous and logic-offending way of bringing your presentation to a close.

There is much more to be said, but this is all I will have to say to you or others on this matter. If you are willing to post this letter on your blog, go ahead and ask the Gaines Center to release the video as well. I have no objections now that I have had the opportunity to present my reservations to possible viewers.

Sincerely,

John Haught

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1. I'm looking for articles from anyone who thinks that Haught did a good job of making the case for compatibility. Post a link in the comments.

Haught vs Coyne: "Science and Religion: Are They Compatible?"

John Haught and Jerry Coyne "debated" the topic of compatibility at the University of Kentucky on October 12, 2011. If you are interested in this topic you MUST watch the entire video AND the question and answer session.¹

This is a classic confrontation between a "sophisticated" theologian and a scientist who knows what religion really is (in South Chicago).

The sophisticated theologian is John Haught, a Roman Catholic (with all that implies). His talk consisted largely of the claim that there are many different layers of explanation. According to Haught, science, by definition, can only address one layer—the naturalistic layer. He claims that he and his fellow theologians are "explanatory pluralists" whereas atheist scientists are "explanatory monists."

By implication, it's better to be an explanatory pluralist IF THE MULTIPLE LAYERS OF EXPLANATION ACTUALLY EXIST. Haught offers not one iota of evidence for the existence of those multiple layers beyond a childish story about boiling water to make tea. (It's the same story he used in the Kizmiller v. Dover trail.)

Haught does not address alternative definitions of science even though a bit of homework would have shown him that Jerry Coyne doesn't accept his definition of science. Apparently, Haught didn't do his homework. This is surprising since Haught's entire case depends on accepting the idea that science and religion are compatible because science can't address the supernatural. In other words, compatibility by fiat.

You'd think that a "sophisticated" theologian would be prepared for someone who challenges that definition. Haught wasn't prepared. In fact, even during the Q&A he doesn't seem to have grasped the problem.

Haught conveniently "forgets" to mention anything about his religious beliefs other than that they involve personal revelation (faith). He doesn't tell us what he believes about transubstantiation, miracles, the virgin birth, the efficacy of prayer, the resurrection, the existence of a soul, heaven, hell, angels etc. That's a shame because Jerry Coyne addresses most of those beliefs and argues that they are incompatible with science. Haught will only reveal (in the Q&A) that he doesn't believe in any of the things Coyne addressed in his presentation. One wonders if Haught is really a Roman Catholic.

I'm getting pretty disgusted with those "sophisticated" theologians who hide behind fuzzy notions of religion when you know damn well they believe in a personal god who intervenes in the world. Haught has been playing this game for decades. Either he's a deist—in which case he should come right out and admit it—or he believes in a personal god who does things that possibly conflict with science—in which case he should have the courage to defend his beliefs.

2011 Bale Boone Symposium - Science & Religion: Are They Compatible? from UK Gaines Center on Vimeo.

Science and Religion: Are They Compatible? October 12, 2011 Q+A with Jerry Coyne and John Haught from UK College of Arts & Sciences on Vimeo.

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1. There's a special treat in store for those who watch the Q&A. You will get to see an incredibly stupid first question from the moderator. I don't think I could have restrained myself the way Jerry Coyne did.