Molecular evidence supports the evolution of the major animal phyla

For those of you who are interested in the evolution of the major animal phyla, let me introduce you to the topic.

See the little red circle on the phylogenetic tree on the right? That's what we're talking about.

Most of the major animal phyla are first observed as primitive fossils in the Cambrian about 540 million years ago. The fossils cluster around dates that only span a few million years (about 10 million years). This is the Cambrian Explosion (see little red circle).

There's considerable debate among evolutionary biologists about what caused this relatively rapid appearance of diverse and disparate large fossils. Intelligent Design Creationist, Stephen Meyer decided that such a debate casts serious doubt on evolution as an explanation for the history of life so he wrote a book called Darwin's Doubt.

Why does Evolution News & Views not allow comments?

The Discovery Institute blog, Evolution News & View (sic) doesn't allow comments. They're beginning to feel a bit guilty about that so there have recently been two posts on the topic.

David Klinghoffer says: Why No Comments at Evolution News?

Michael Egnor writes: Comments by Darwinists: Another Perspective

The problem from their perspective is that their opponents are rude, crude, and abusive so they have to ban all comments. Here's how David Klinghoffer puts it.

So what are we supposed to do when, under a free-for-all commenting policy, Darwinists like Moran -- who is far from scraping the bottom of the barrel as far as online evolutionists go -- post abusive, defamatory, and false comments on our own news site? Should we delete their comments? Edit them? But then we would be accused of "censorship."

Should we perhaps allow them to say whatever they like, fouling the carpet in our own living room? When they have every opportunity to write what they like where they like and receive an answer from us, if the challenge rises to the level of being worthy of a reply? Why in the world would we do that?

If we can't accept providing a free forum for a great deal of nasty, false, and vacuous chatter, the only alternative is to devote significant time to moderating the forum, policing the sandbox, and then defending that moderation at every step as it is challenged. That would require staffing that we can't afford.

The problem with that line of reasoning is that there already is an ID blog that allows comments. Check out Uncommon Descent to see who's fouling the carpet.

What they're really worried about isn't the "Darwinists." It's Mung, bornagain, Vy, Andre, Virgil Cain, Upright BiPed, Mapou and others like them who will dominate the comments section and give the Discovery Institute a bad reputation.

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Intelligent design needs to clean up its act if it expects to be taken seriously

Jonathan McLatchie tried to make the case that ID is different from creationism in two recent videos on a Christian apologetics podcast [see Jonathan McLatchie says that intelligent design is a science and Jonathan McLatchie explains the difference between intelligent design and creationism].

I think there's some serious attempts to do science among ID proponents but I also think it's bad science. It's fun, informative, and challenging to debate real science with knowledgeable, informed members of the ID community.

However, that same community embraces many, many advocates who are not knowledgeable about evolution and not informed about how science works. They are not scientists by any stretch of the imagination but they pretend to be scientific. Many of them are Young Earth Creationists who seriously think that the universe was created pretty much as it is only 6000 years ago. While it's true that every ID proponent is a creationist (i.e believes in the existence of a supernatural creator) there are some versions of creationism that are more irrational than others.

The theistic evolution version of creationism rejects the views of their anti-science YEC friends but Intelligent Design Creationism embraces all comers as long as they are vehemently opposed to materialism and evolution. That's fine, but then ID can't claim to be scientific. You can't have your cake and eat it too. Either you try to act like scientists, in which case you have to oppose the kooks and YECs in your movement, or you admit that you are a religious and social movement, in which case you stop pretending to be a science.

I hope that the knowledgeable, informed, members of the ID community will abandon the ridiculous path they've taken where they try to make a scientific case for ID knowing full well that the majority of their supporters disagree strongly with their premises (e.g. common descent). That's an untenable position.

We've seen recently that some ID proponents are attempting to do this. I'm thinking of Jonathan McLatchie and Vincent Torley right now but there are others. How is it working out? Look at the Torley post on Uncommon Descent where he's trying to explain evolution to IDiots: Human and chimp DNA: They really are about 98% similar. It's an uphill battle. The kooks are accusing him of becoming a Darwinist.

But that's exactly what the ID community needs to do in order to gain credibility. They need to shed the kooks and the IDiots who make them look silly. When they do that, they may find that more of us are willing to have a serious discussion about science.

David Klinghoffer is one of the names I mentioned in an earlier post when I identified leading ID proponents who have no clue about the science they are opposing. Others are Denyse O'Leary, Barry Arrington, Phillip Johnson, Casey Luskin,¹ David Klinghoffer, Paul Nelson, John West, and William Lane Craig. These people represent the face of the ID movement and that's how we're going to judge Intelligent Design Creationism unless they clean up their act. (We also judge it by the people who post comments on blogs and Facebook and by those politicians who support it in the public sphere.)

Klinghoffer posts on Evolution News & Views (sic)—a site that doesn't allow comments. His latest post is a classic example of the problems that the ID movement faces: Here's Why We Answer Some of Our Less Cogent Critics.

As you can see, he avoids the issue I raised in favor of an ad hominem attack. Wouldn't it be nice to see a scientific debate between Michael Behe and David Klinghoffer on the meaning of evolution? Not going to happen as long as ID is primarily a religious movement.

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1. Casey Luskin can't decide how old the universe is but he leans toward Young Earth Creationism. Yet he's a leading spokesman for the "science" of intelligent design.

The quality of the modern scientific literature leaves much to be desired

Lately I've been reading a lot of papers on genomes and I've discovered some really exceptional papers that discuss the existing scientific literature and put their studies in proper context. Unfortunately, these are the exceptions, not the rule.

I've discovered many more authors who seem to be ignorant of the scientific literature and far too willing to rely of the opinions of others instead of investigating for themselves. Many of these authors seem to be completely unaware of controversy and debate in the fields they are writing about. They act, and write, as if there was only one point of view worth considering, theirs.

How does this happen? It seems to me that it can only happen if they find themselves in an environment where skepticism and critical thinking are suppressed. Otherwise, how do you explain the way they write their papers? Are there no colleagues, post-docs, or graduate students who looked at the manuscript and pointed out the problems? Are there no referees who raised questions?

Ten years after Dover - an excellent decade for Intelligent Design Creationism?

This month marks the tenth anniversary of the Kitzmiller v. Dover case in Pennsylvania [Tammy Kitzmiller, et al. v. Dover Area School District, et al.]. The legal victory will be celebrated by NCSE and Panda's Thumb and by many other supporters of science and evolution. If American law is your thing, then please join in the celebration of a legal victory.

It's much more interesting to evaluate whether the legal victory in Pennsylvania had any significant effect on the general public. Did it cause people to change their minds and abandon Intelligent Design Creationism to embrace science? Has America moved closer to the time when real science can be taught in the schools without interference from religion? Have politicians stopped trying to water down evolution in the public schools because of Judge Jones' decision in Kitzmiller v Dover? Have politicians stopped opposing evolution and has the public stopped voting for those who do?

How can she go wrong?—let us count the ways ...

There's a very good reason why the creationist website Evolution News & Views (sic) doesn't allow comments but that won't stop us from making comments on Sandwalk. Check out Ann Gauger's latest offering at: Waiting for Mutations: Why Darwinism Won't Work.

There are a few errors in that post. How many? Let us count the ways.¹

Theme
Mutation
-definition
-mutation types
-mutation rates
-phylogeny
-controversies
What's interesting about that post is that we've been over the data many times in an attempt to explain mutation to the creationists. Last year I tried to explain why humans and chimpanzees have accumulated about 22 million point mutations since the time they evolved from a common ancestor about 6 million years ago. I thought it would be helpful if they understood why these numbers are perfectly reasonable according to population genetics.

What happened was that the vast majority of commenters on Uncommon Descent called me names and told me I was wrong. A few creationists, Sal Cordova, Vincent Torley, and Branko Kozulic took up the challenge and, for a short while I thought they understood.

Debating Darwin's Doubt: the prequel

I've had a chance to read most of Debating Darwin's Doubt and, as I mentioned earlier today, it doesn't address any of my criticisms. Here's the list of my blog posts ...

• Darwin's Doubt: A Synopsis
• Darwin's Doubt: The Genes Tell the Story?
• The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes
• Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates
• Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates
• Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"
• Stephen Meyer Says that "Homology" Is a Problem in Molecular Evolution

I'm really jealous because the IDiots spend a lot of time on Nick Matzke's blog post and on other posts.

I can only assume that they have no rebuttal. I know they read my blog and they should have been on the look-out for my critique in September 2013 because David Klinghoffer specifically challenged me to review Darwin's Doubt.¹ [On Darwin's Doubt, Still Waiting to Hear from Big Shots in the Darwin Brigade]. Here's what he said on September 4, 2013 just before I put up those posts.

Inside the mind of an Intelligent Design Creationist

The blog Evolution News & Views (sic) is part of the public outreach of The Center for Science and Culture, a subsidiary of the The Discovery Institute.

Ann Gauger is a researcher at The Biologic Institute, which is funded by The Discovery Institute. She wrote an article for Evolution News & Views entitled What If People Stopped Believing in Darwin? I think it's safe to assume that this is a common view of a leading Intelligent Design Creationist and close to the position of other members of that cult.

How do Intelligent Design Creationists deal with pseudogenes and false claims?

Some of the people who comment here have pointed out that this is the second anniversary of a post by Jonathan McLatchie on Evolution News & Views (sic): A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene.

That post is significant for several reasons. Let's review a bit of background.

Intelligent Design Creationists have a problem with pseudogenes. Recall that pseudogenes are stretches of DNA that resemble a gene but they appear to be non-functional because they have acquired disruptive mutations, or because they were never functional to begin with (e.g. processed pseudogenes). All genomes contain pseudogenes. The human genome has more than 15,000 recognizable pseudogenes.¹ This is not what you would expect from an intelligent designer so the ID crowd tries to rationalize the existence of pseudogenes by proposing that they have an unknown function.

Insulators, junk DNA, and more hype and misconceptions

The folks at Evolution News & Views (sic) can serve a very useful purpose. They are constantly scanning the scientific literature for any hint of evidence to support their claim about junk DNA. Recall that Intelligent Design Creationists have declared that if most of our genome is junk then intelligent design is falsified since one of the main predictions of intelligent design is that most of our genome will be functional.

THEME

Genomes & Junk DNA
They must be getting worried because their most recent posts sounds quite desperate. The last one is: The Un-Junk Industry. It quotes a popular press report on a paper published recently in Procedings of the National Academy of Sciences (USA). The creationists concede that the paper itself doesn't even mention junk DNA but the article in EurekAlert does.

An accomodationist defends the science of the Pope in the journal Nature

I don't think scientific journals or scientific organizations should take a position on the conflict between science and religion but that doesn't mean they should stay away from the subject altogether. The journal Nature has just (July 28, 2015) published a defense of accomodationism written by David M. Lodge [Faith and science can find common ground]. Lodge describes himself as a "Protestant ecologist embedded for 30 years in a Roman Catholic university." The Catholic University is Notre Dame [see David M. Lodge].

His main argument is that the current Pope understands the science of the environment and has spoken out in favor of protecting the environment. David Lodge thinks this represents an accomomodation between science and religion.

I never expected this!

David Klinghoffer writes at Evolution News & Views (sic): In The New Yorker, Tom Wolfe Compares Persecution of Intelligent Design Advocates to the "Spanish Inquisition".

Interviewed by The New Yorker earlier this year, the great novelist and journalist Tom Wolfe acknowledged that he's writing a book about evolution -- actually, "a history of the theory of evolution from the nineteenth century to the present." No indication of what his overall thesis might be, but he "invokes the Spanish Inquisition when discussing how academics have cast out proponents of intelligent design for 'not believing in evolution the right way.'"

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Debating Darwin's Doubt

Today is the day that John Scopes was found guilty in Dayton, Tennessee (USA) 90 years ago. The Intelligent Design Creationists have marked the day with publication of a new book called Debating Darwin's Doubt [A Scientific Controversy That Can No Longer Be Denied: Here Is Debating Darwin's Doubt].

The book was necessary because there has been so much criticism of the original Stephen Meyer's book Darwin's Doubt. David Klinghoffer has an interesting way of turning this defeat into a victory because he declares,

... the new book is important because it puts to rest a Darwinian myth, an icon of the evolution debate, namely...that there is no debate, about evolution or intelligent design!

The creationism continuum

Intelligent Design Creationists often get upset when I refer to them as creationists. They think that the word "creationist" has only one meaning; namely, a person who believes in the literal truth of Genesis in the Judeo-Christian Bible. The fact that this definition applies to many (most?) intelligent design advocates is irrelevant to them since they like to point out that many ID proponents are not biblical literalists.

There's another definition of "creationist" that's quite different and just as common throughout the world. We've been describing this other definition to ID proponents for over two decades but they refuse to listen. We've been explaining why it's quite legitimate to refer to them as Intelligent Design Creationists but there's hardly any evidence that they are paying attention. This isn't really a surprise.

The moral argument for the existence of gods

It's Sunday. I assume that most of you are at church but here's something for the rest of you. It's a sermon by William Lane Craig on The Moral Argument for the Existence of Gods. I found the link on Evolution News & Views (sic) a blog that's devoted to the "science" of Intelligent Design Creationism [Watch: Three from William Lane Craig]. I'm not sure what this has to do with evolution except that the word is mentioned a few times in the videos.

I'm also not sure what this has to do with intelligent design since, as we all know, the "science" of intelligent design has nothing to do with gods.

Kirk Durston appears on Evolution News & Views to announce that "Darwinian Theory" has been falsified

Kirk Durston is a Canadian biophysicist with a Ph.D. from the University of Guelph (Guelph, Ontario, Canada). He's been attacking evolution for more than a decade using all the old tricks and sophistry that we've come to expect from creationists.

I thought you might be interested in his latest attempt to discredit evolution. His post is at: An Essential Prediction of Darwinian Theory Is Falsified by Information Degradation.

He begins by claiming that "Darwinian Theory" (what ever that is) makes an essential prediction. It predicts that information must increase over time.

In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.

An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.

The ugly face of Intelligent Design Creationism

Intelligent Design Creationists like to pretend that their particular version of creationism is scientific. They claim they have evidence of an intelligent designer (gods), but 99% of their literature is an attack on evolution and not a defense of a new scientific theory. Those attacks take many forms but the worst ones are the attempts to smear Darwin and associate evolutionary biology with racism and the holocaust.

David Klinghoffer continues this despicable tradition in his latest post on Evolution News & Views (sic): In Explaining Dylann Roof's Inspiration, the Media Ignore Ties to Evolutionary Racism. Klinghoffer discusses the views of Dylann Roof, the man who shot and killed nine people in a church in Charleston, South Caroline (USA). Dylann Roof is reported to be a devout Christian [Dylann Roof was a devout Christian] but that's not relevant.

Of course, no one I've referred to endorses Dylann Roof's murderous rampage. I don't doubt that they are all sincerely mortified by the association, however unintended, with such unapologetic, undisguised evil.

I mention this at all not to blame them for Roof's crime, in any way, but simply to note -- because the mainstream media covers it up -- how certain ideas tend to hang together.

The racial elements in Charles Darwin's writing, the eugenicist implications, are often brushed aside as ugly but incidental, a mere byproduct of his time and place. Yet the myth of European superiority over inferior dark peoples continues to percolate in some evolutionary thinking, a century and more after the close of the Victorian era. It seems to have found an eager student in a disturbed young man named Dylann Roof.

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The science behind Intelligent Design Creationism

I do not agree with those who dismiss Intelligent Design Creationism because it is not science. I prefer to think of it as an approach that superficially resembles the scientific approach but fails in various ways. In this sense, it's not much different from lots of other bad examples of science.

Let's look at the way Intelligent Design Creationists describe their attempt to be scientific. This is from a recent post by that well-known scientist,¹ Casy Luskin, on Eovlution News & Views (sic) [Does Intelligent Design Deserve Academic Freedom?]. In that post, Luskin lists four criteria proving that ID is a genuine scientific theory.

• Uses the scientific method to make its claims,
• Is backed by credible scientists,
• Is supported by credible peer-reviewed scientific publications,
• And uses arguments that stand up to scrutiny, and are backed by evidence.

It's the first point on the list that I want to discuss. The link takes you to a brief description of how Intelligent Design Creationism uses the scientific method to prove that gods played a role in the history of life. Here's how it works ...

Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Poor James Lunney resigns from the Conservative Party because of bullying over his religious beliefs

Some of you may recall James Lunney, Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia. He's a chiropractor who spoke out against evolution back in 2009 [James Lunney: Creationist, Chiropractor, Conservative].

More recently, he defended another MP who didn't believe in evolution. He was mocked and ridiculed in the popular press and now he has decided to resign from the Conservative Party and sit in the House of Commons as an Independent. That's not working out so well according to CBC News [James Lunney defends views on evolution in House of Commons].

One day after he announced he was leaving the Conservative caucus to better defend his religious beliefs, Nanaimo-Alberni MP James Lunney attempted to do just that from his new seat in the corner of the House of Commons reserved for independent MPs.

But despite his best efforts, he was unable to convince House of Commons Speaker Andrew Scheer that the "cyberbullying" and "crowd-shaming" that he claimed to have experienced after questioning the science behind evolution constituted a breach of his parliamentary privilege.

Imagine that! He was unable to convince Parliament that making fun of his silly beliefs is wrong! This is exactly how the Canadian public SHOULD deal with people who act like kooks.

Wanna hear about his beliefs? This is what he said in Parliament ....

Speaking to CBC News Power & Politics host Evan Solomon on Wednesday evening, Lunney said that he was tired of seeing his faith community bullied.

...

Lunney described evolution — or, as he calls it, "macro-evolution" is "a theory in crisis."

"Scientists are not able to speak their mind on that — at least half of them who feel this way, they're gagged by an old construct," he argued.

"There's a whole generation of kids being taught that what they're taught in Sunday School or in church is garbage, it's wrong, it's false, and it's simply a form of bullying that's no longer acceptable. It's not scientifically tenable, it's a disservice to science… it's not freedom of religion if your views are put down by your peers."

Freedom comes in several forms. If you live in a free society then you have to be prepared to accept criticism of your most cherished beliefs. You can't hide behind religion to protect you when you act like an IDiot. Pointing out the stupidity of a Member of Parliament is not bullying

As far as I'm concerned, this is exactly how freedom should work.

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