The Third Fourth? Way

Back in 1997, James Shapiro wrote an article for the Boston Review entitled "A Third Way." It was a very confusing article. His main point seemed to be that conventional neo-Darwinism wasn't a complete picture of modern evolutionary theory.

That part wasn't news since by 1997 the ideas of Neutral Theory and random genetic drift had been around for thirty years. Apparently, Shapiro was three decades behind in his understanding of evolution.

Shapiro doesn't demonstrate that he understands population genetics and random genetic drift. This just one (of many) criticisms that I mentioned in my review of Shapiro's book Evolution: A View from the 21st Century in NCSE Reports [Evolution: A View from the 21st Century]. Shapiro responded to my review at: Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century] and I discussed his response on my blog [James Shapiro Responds to My Review of His Book].

The "third" way, according to Shapiro's 1997 article, is not classic Darwinism and it's not creationism. Instead, it's a new way of looking at evolution.

What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?

Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.

Now Shapiro has joined forces with some other "revolutionaries" and started a new website called "The Third Way." It has grandiose goals ....

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.

There's only one problem. I'm familiar with Shapiro's ideas and with the ideas of most of the other people listed on the website and I don't think any of them (except Eugene Koonin) have anything significant to say about evolutionary theory. Futhermore, most of them don't seem to understand that there's already been a revolution and population genetics, Neutral Theory, etc. won the day. They seem to have completely missed that revolution.

They are advocating a fourth way that skips right from adaptationism to something else.

They are like a group of would-be revolutionaries marching up Rue de Lyon in Paris only to discover that the Bastille has been replaced by an open square and an opera house.

Note: There aren't many biologists that are interested in this "Third Way" but the creationists are lapping it up [A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology Have Launched a New Website; Welcome to Them!].

---

More primordial soup nonsense

I just discovered a new paper on the origin of life (Keller et al. 2014). The authors think they are looking at the first primitive biochemical pathways, which they identify as glycolysis and the pentose phosphate pathways.

Here's what they did. They took a bunch of pure sugar phosphates¹ and dissolved them in water containing salts and metal ions that were likely present in the primordial oceans. They heated the solution up to 70° C and looked at the degradation products. Low and behold, the sugar phosphates degraded and sometime the products were other intermediates in the glycolytic and pentose phosphate pathway, including pyruvate and glucose.

They conclude that ...

Little Richie Dawkins

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.

Stephen A. BatzerHere's a video that was posted today on Uncommon Descent by Salvador Cordova. Before watching it, read my post on: Why are Darwinists do uncivil?. It links to an IDiot post by Stephen A. Batzer where he complains about "Darwinists" being uncivil.

Here's one of the points that Batzer makes ...

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.

The video was produced by Mike Booth. Decide for yourself if the evolution side of the debate behaves like the IDiots. (Apologies to Richard Dawkins for propagating this nonsense but people need to see the depths to which the Intelligent Design Community can sink.)


UPDATE: Denyse O'Leary has responded to this post [Huh? Actually, we thought Little Richie (Dawkins) was a special creation, just for us…]. She says, "Moran thinks it originated in the ID community. Unclear why because it’s really not about our usual questions and concerns." Actually I don't know anything about Mike Booth or whether he is a support of Intelligent Design Creationism. I looked, but I couldn't find anything. What I do know is that IDiots like Denyse O'Leary post the obnoxious video on their websites. O'Learly also says this about the video, "It’s also not a lot nastier than the old showman himself." I think I'll let intelligent people decide for themselves who is nastier. I'm glad that Denyse O'Leary at least acknowledges that the video she posted was nasty.

---

Why Are "Darwinists" So Uncivil?

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].

1. They're human. That says a lot that's negative about them and of course about us, too.
2. 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.
3. You are challenging their religious beliefs, which they know, just know, to be true.
4. 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.
5. "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.
6. 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.

---

John Witton Will Pay You $1000 to Answer One of His Questions

John Witton doesn't know much about biochemistry, genetics, or evolution but he's willing to learn. He will pay you $1000 (US) if you can answer any one of the six questions he has posed. He made this offer in the comments to my post: Saturday, February 28, 1953.

Here's what he said ...

I have been known to cause some problems on other forums, for obvious reasons, but I had hoped that on this forum we will be able to get to the bottom of the problems such as" vitalism vs entropy barrier, self assembly of proteins, self-cell membrane formation, metabolism first vs RNA world, why did evolution need 600 types of mangoes and how did they evolve and why?

Why did Larry Moran and Craig Venter evolve to baldness only on the part of the scalp but they have retained their bushy hair on the side and lower back of their scalp????

For those who answer one of these question logically, I am willing to pay $1000.00

I offered to answer two questions; the one on self assembly of proteins and the one on why male pattern baldness evolved. I suggested that John Witton could send the check to a neutral third party and that we could agree on a judge who would decide whether I had answered the questions satisfactorily. I recommended Michael Behe as the judge for the first question and Michael Denton as the judge for the second question.

John Witton agreed. On Saturday, March 2, 2013, he said ...

I’m glad you took the bait Larry…for the lack of better word in English… You are not a very good bluffer though…I’m hoping you don’t play poker and bet large sums of money… Anyway, even though you are paddling back from some of the issues I have presented you know you can’t explain, I’m still going to pursue this transaction, since I can still nail you on those two issues you feel comfortable with…You have nothing to lose...or it might be a little bit of pride, which is fine with me… So, this is what I’m doing. I am sending two cheques $1000.00 US each to Michael Behe and Michael Denton with the explanation of our agreement. They may not like writing extensive explanation as to their judgment or nothing at all, except Larry or John is the winner in their view. We just have to accept that.

Then on Monday he said ...

I have contacted both Behe and Denton. I have emailed the Discovery Institute regarding our arraignment. Even The Star is interested, if Behe participates... I don't think anybody takes you seriously Larry... We'll see.. You seem to be a big mouth that writes text books nobody understands, even you ...;)

I checked with Michael Behe on Thursday but he still had not heard from John Witton. I wasn't able to find out how to contact Michael Denton ... I'm waiting for Witton to send me the contact information since he already got in touch. (If anyone has an email address please send it to me.)

As it turns out. Witton had the stomach flu so he didn't send the checks. I'm sure he'll send them as soon as he feels better. (Apparently the flu strain comes from Canada!)

Larry is right. I have not sent the cheques or the paper to Behe or Denton yet... I'm sick with a bad case of stomach flu...You don't have to believe me... I will try to contact you when I'm better...Sorry to all my supporters...

According to Witton he now "got Larry by the balls." I thought I should let all my enemies know about this so they can watch the spectacle. Some Sandwalk readers might want to help John by answering one of the other questions for $1000.

While we're waiting for John Witton to keep his word, you might enjoy this video of Robert Shapiro (not John Witton) questioning the work on the origin of life. It was posted by John Witton so presumably he likes it.

---

James Shapiro Responds to My Review of His Book

I reviewed Shapiro's book, Evolution: A View from the 21st Century for NCSE reports. (NCSE = National Center for Science Education.) You can read it here.

James Shapiro has responded to my review in the latest issue of NCSE reports: Reply to Laurence A Moran’s review of Evolution: A View
from the 21st Century.

Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...

Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists¹]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!

James Shapiro Never Learns

One of the remarkable things about kooks is that they are incredibly resistant to learning from their mistakes. James Shapiro gives us a fine example in one of his latest articles on The Huffington Post where he tries to convince us that the old definition of "gene" has outlived its usefulness. According to Shapiro, "DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function."

Really? While we all can agree that there's no definition of "gene" that doesn't have exceptions, we can surely agree that some definitions work pretty well. I've argued that defining a gene as, "a DNA sequence that is transcribed to produce a functional product" works well in most cases [What Is a Gene?].

Let's see how James Shapiro handles this problem.¹ He says,

The identification of DNA as the key molecule of heredity and Crick's Central Dogma of Molecule Biology [Crick 1970] initially seemed to confirm Beadle and Tatum's "one gene -- one enzyme" hypothesis.

I've already explained that Shapiro doesn't understand the Central Dogma of Molecular Biology even though he quotes the Francis Crick papers that explain it correctly [Revisiting the Central Dogma in the 21st Century]. I also made this point in my review of his book: Evolution: A View from the 21st Century.

How Do Intelligent Design Creationists Define "Creationism"?

David Klinghoffer showed up in the comments on James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle" to ask about creationism.

He didn't like the fact that I define "creationism" as belief in a creator and anyone who believes in a creator is a creationist. I identified several flavors of creationism including Young Earth Creationism, Intelligent Design Creationism, and Theistic Evolution Creationism. This is exactly the same sort of definition used by many people and it's the one described in the Wikipedia article on creationism. (It has even more flavors.)

David Klinghoffer didn't like that so he decided to make an issue of it by posting on Evolution News & Views: What Is a "Creationist"? Let's take a look at what he says in order to learn a little more about the creationist mindset.

Does the Central Dogma Still Stand?

Lots of people don't understand the Central Dogma of Molecular Biology and that's probably why there are so many articles announcing its death. The article and book by James Shapiro is just one example [Revisiting the Central Dogma in the 21st Century].

The correct version of the Central Dogma of Molecular Biology is .... [see Basic Concepts: The Central Dogma of Molecular Biology]

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)

Eugene Koonin has an article in Biology Direct entitled Does the central dogma still stand (Koonin, 2012).

Groupthink Science And That 'Junk DNA'

The IDiots (e.g. Tom Bethell) over at Evolution News & Views are gloating about a comment made on The Wall Street Journal website [Why ENCODE Is a Significant Defeat for Darwinism].

The WSJ article is: Groupthink Science And That 'Junk DNA'.

Anyone with even the slightest understanding of the evolutionary process knows that evolution is too relentlessly efficient to have allowed most, or even large sections, of DNA to be "junk" ("'Junk DNA' Theory Debunked," U.S. News, Sept. 6). Any intelligent scientist would have simply said, "I don't know."

Unfortunately, this says something important about the quality of contemporary Ph.Ds. Groupthink has become pervasive in part because of how research is now financed: grants. The disillusioning sociological aspects of scientific research that Thomas Kuhn identified more than four decades ago have become more pronounced, not less.

Tom Shillock

Portland, Ore.

This is exactly backwards, in my opinion. The real problem is that many scientists think, incorrectly, that natural selection would have removed all junk DNA so they are looking for reasons why it isn't junk. If they can't find evidence then they just make up a story or re-define the word "function." They don't have even the slightest understanding of evolution, just like Tom Shillock.

UPDATE: Shapiro and Sternberg Anticipated the Fall of Junk DNA.

---

James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"

Do you remember James Shaprio? He's the University of Chicago scientist who claims to have discovered a new theory of evolution in his book evolution: A View from the 21st Century [see my review in NCSE Reports]. The book criticizes the old hardened version of the Modern Synthesis and never mentions things like random genetic drift or Nearly-Neutral Theory. It's difficult to imagine how someone could criticize evolutionary theory without understanding population genetics but he managed to pull it off.

You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.

How to Get Banned on Sandwalk

I try really hard not to ban anyone from commenting on Sandwalk but there are some things I will not tolerate.

Someone named David Roemer recently tested the limits of my patience, and failed. He is now banned.

Here's what happened. I received an email message from David Roemer about a comment of his that did not appear on Sandwalk. I don't know why it didn't appear. I don't remember seeing it.

Shortly after receiving the email message I received a copy of a message David Roemer sent to the chair of my department. Here's the beginning ...

Dear Dr. XXX,

Prof. Moran, I believe, didn't approve of the following comment I made on his Sandwalk blog. He has every right to do so, but he has a moral duty not to coverup the misinformation contained in the AJP article I mention in my censored comment:

Natural selection only explains the adaptation of species to the environment. Not enough is known about the innovations natural selection acts upon to understand how mammals evolved from bacteria in only 3.5 billion years (common descent). The only theory that attempts to explain common descent is ID, but there is no evidence for ID.

IDiots try to make their theory look better by comparing it with natural selection. Atheists go along with this scam because they don’t want to admit that ID is a better theory than natural selection in some sense.

A corollary of the limitations of natural selection is that the second law of thermodynamics doesn’t apply to evolution, just as it doesn’t apply to the evolution of stars. Nevertheless, there is scientific literature about whether evolution violates the second law. Authors on the “does not” side argue that heat energy from the sun accounts for the increase in order (decrease in entropy). Heat, of course, tends to increase disorder.

This nonsense reached an extreme level in an article published by the American Journal of Physics (Entropy and evolution, Nov. 2008). This article actually calculates the entropy of the biosphere using the Boltzmann constant and an estimate of the thermodynamic probability of life. I’m trying to get the AJP to retract this absurd article.

I'm copying David Novak because he is on the Institute Board of First Things, which is refusing to publish my attached essay explaining why the AJP article is absurd. Both Novak and Moran are helping the AJP lie about evolution and thermodynamics.

My chair will be amused by this sort of thing. There's nothing he could do about it even if he wanted to.

This is one of the criteria for banning. Anyone who tries to get someone fired or reprimanded by going over their head to their employer will be banned. Anyone who harasses the family and friends of someone they disagree with will be banned. There are no exceptions.

I've also banned John Kwok for doing the same thing in an attempt to silence Jim Shapiro.

---

My Review of Shapiro's Book Is Finally Published!

I wrote a review of Evolution: A View from the 21st Century for NCSE (National Center for Science Education). It was finished last September but NCSE delayed publication until they fixed up the website for Reports of the National Center for Science Education.

Here's the Table of Contents of the latest issue. All articles are free!

Shapiro threatens to respond to my review if he doesn't like it. I'm certain he won't like it. I'm looking forward to seeing how he responds to my criticisms, especially concerning his lack of knowledge of the history of evolutionary theory and his confusion about the meaning of the Central Dogma of Molecular Biology.

---

What Does James Shapiro Think?

James Shapiro is one of those scientist who think that evolutionary theory is due for a "paradigm shift." His schtick is that mutations often involve genome rearrangements and that reorganization of the genome may be a sort of "natural genetic engineering" that cells use to direct evolution. It's hard to figure out what Shapiro actually means and even harder to figure out his motives. I posted an earlier comment from him that suggests he is looking for a middle ground between science and Intelligent Design Creationism. Here's part of that earlier post: The Mind of James Shapiro

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.

Now Susan Mazur has gotten into the game of trying to figure out James Shapiro. You may recall that Susan Mazur has made a minor career out of touting the upcoming revolution in evolutionary theory. Here are some excerpts from her interview with James Shapiro on a website called Counterpunch: The Evolution Paradigm Shift.

Suzan Mazur:... Are Coyne and his pal Richard Dawkins, by not publicly recognizing that a sea change has occurred, milking lucrative performances and book deals? And if so, isn’t this a disservice to science?

James Shapiro: Well that’s a loaded question.

I’ve gone on record in my blog as saying that I thought that Dawkins and his ill-conceived atheist crusade hurts science education and hurts evolutionary science. I’ve criticized Jerry Coyne for making statements that he can’t support. Both Coyne and Dawkins have been characterized as having a neo-atheist agenda in attacking religion. And it is true that many of the comments on my blog reflect a deep reservoir of anti-religious sentiment. I’ve noted in the blog that we should get out of the business of attacking supernaturalists. It’s not in science’s interest to make a war with religion or religious belief.

Suzan Mazur: And get on to the science.

James Shapiro: And get on with the science. And also to have a little bit of humility. Science never provides ultimate answers.

Both Coyne and Dawkins are doing well for themselves by being vitriolic and vehement in their campaign against religious belief and against some of the more foolish things that religious fundamentalists do. But I suspect ego gratification is the major driver more than financial gain. Obviously it’s nice if you make money at the same time.

This appears to be a typical accommodationist position, assuming that Shapiro is an atheist. I just wish he'd be a little more up front about his stance.

James Shapiro: ...The moth cover was ultimately chosen because the kind of exquisite mimicry it represents is an evolutionary puzzle.

How does that come about? I think gradualist explanations are difficult to sustain in the case of mimicry. Recently it’s been discovered that there are master control regions, sort of like Hox complexes but more complicated, that control wing patterns in butterflies. I suspect as people analyze those we’ll know more about how the mimetic patterns evolved.

The book hasn’t been reviewed by any of the major journals yet. Nature and Science have not reviewed it. The National Center for Science Education is reviewing it in June. I’m interested to see whether they want to show that evolution science is alive and doing novel and controversial things.

As I said in my blog, science is not doing very well in this evolution vs. religion dispute. I think part of the reason why we’re doing poorly is that the most recent and exciting science is not being presented to the public. Clearly, the issues are not being presented in a way that shows evolution science isn’t stuck in ideas from the last century and the last century before that.

I wrote the review that will soon appear on the NCSE site. I can assure him that I'm well aware of many exciting developments in evolutionary theory. The ones that are important (population genetics, random genetic drift, Neutral Theory, punctuated equilibria, speciation) are ones that Shapiro doesn't understand or mention in his book. (Gould isn't even in the index!) The ones that are trivial and were dismissed as minor embellishments decades ago are the ones that, in his mind, are going to cause a paradigm shift.

---

James Shapiro Publishes on Evolution News & Views

James A. Shapiro, author of Evolution: a View from the 21st Century has been criticized for being an Intelligent Design Creationist, or at least a sympathizer. He denies it but his denials sound very much like someone who protests too much.

Shapiro has now been allowed to post an article on the main IDiot blog, Evolution News & Views [A Response to Ann Gauger's and Douglas Axe's Comments. I don't agree with his response but that's not the point. Do you know any respectable evolution supporter who would post on a creationist blog?

Can you imagine his University of Chicago Colleague, Jerry Coyne, posting an article on the flagship blog of the Discovery Institute?

---

False Dichotomy

 

A false dichotomy is when you are presented with two choices and told that if one is wrong then the other must be correct but there are actually other choices.

Intelligent Design Creationists are very fond of this argument. They tell you that there are only two choices when it comes to explaining biology: either Darwinism or Intelligent Design Creationism. If a given feature of the biological world cannot possibly be explained by Darwinism, then God must exist and he must have designed the feature.

Here's Douglas Axe illustrating the false dichotomy on Evolution News & views [Let Science Be the Arbiter: A Reply to James Shapiro].

As an ID proponent, I've put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

There is no crutch here. The aspects of protein structure that appear to preclude a naturalistic origin have been described in detail. If Shapiro or anyone else were to show in detail how these are overcome by a naturalistic mechanism, then my argument would fall and I would let it fall. But the reverse needs to be true as well. Scientists who personally side with naturalism have to be willing to let naturalism fall, as otherwise they would be guilty of using a crutch to prop it up.

This is actually an attempt to get around the charge of false dichotomy by extrapolating from a rejection of Darwinian explanations to any naturalistic explanation. If Axe is truly able to demonstrate that his "data" cannot possibly be explained by any naturalistic means then it follows logically that the only other type of explanation has to be supernatural. But what Axe is really arguing against is a Darwinian explanation and it's only his lack of imagination and arrogance that allows him to claim that no other naturalistic explanation is possible.

As we have seen time after time, the Intelligent Design Creationists do not have a scientific theory or any kind of scientific explanation for biological phenomena. All they have is criticisms of science—criticisms that are usually based on a lack of knowledge. When will we see an ID explanation of protein folding and function?

---

The Mind of James Shapiro

I recently read Evolution: a View from the 21st Century by James Shapiro. It was a very annoying and frustrating experience. I do not recommend this book. I've already posted a rebuttal of his silly claim that the Central Dogma of Molecular Biology needs to be revised [Revisiting the Central Dogma in the 21st Century ]

The really frustrating part was trying to figure out Shapiro's agenda. He clearly has one. Is it just that he's against "conventional evolutionary theory"—whatever that is? Or, is he laying the groundwork for introducing God and intelligent design?

Shapiro denies that he's a supporter of intelligent design yet he published several papers with Richard Sternberg, one of the darlings of Intelligent Design Creationism. Furthermore, he (Shapiro) uses many of the same anti-evolution arguments used by Intelligent Design Creationists.

This prompted Bill Dembski to accuse James Shapiro of "dancing in the DMZ between Darwin and design" [Is James Shapiro a Design Theorist?].

For proponents of intelligent design, James Shapiro's constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.

This got a response from Shapiro that has now been posted on Evolution News & Views ["Is James Shapiro a Design Theorist?": James Shapiro Replies]. Here's what Shapiro says ...

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.

Clear as mud. There's one thing I know for sure: horizontal DNA transfer etc. are perfectly compatible with today's evolutionary thinking. If Shapiro is wrong about this—and he is— then maybe he's also misleading us about his belief in intelligent design creationism.

---

Jonathan Wells Sends His Regrets

Paulmc visited Uncommon Descent in order to defend junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. Now Wells has responded to several of paulmc's points [Jonathan Wells on Darwinism, Science, and Junk DNA].

We'll get to those issues in another post but right now I want to take note of something Wells said at the end of his article.

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

I can understand why Wells might decline to post a comment on Sandwalk. Many of us know what it's like to try and argue with the readers of the intelligent design blogs. Wells would meet the same reception here that we get over there.

But that doesn't preclude Wells from posting on Uncommon Descent or Evolution News & Views. If he really believes that my review of his book is an example of "confused thinking and malicious misrepresentations of my work"¹ then why not back up such a statement with a thoughtful response on a friendly blog? Evolution News & Views would be ideal since comments are banned.

---

1. Wells has accused other scientists of misrepresentation. It's a common theme in The Myth of Junk DNA and in Icons of Evolution. I quoted this passage in Junk & Jonathan: Part 13—Chapter 10.

Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.

I can understand why Wells is reluctant to defend such statements. It's because they are indefensible.

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.

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

---

The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.

In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).

Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)