How not to examine the evolution of proteins

The Discovery Institute has me on a mailing list for their newsletter, Nota Bene. That’s probably unwise: usually I just glance at it, see another ignorant bit of fluff from Luskin or Nelson or one of the other usual suspects, and I snigger and hit ‘delete’, but sometimes they brag about how they’re really doing science, and I look a little closer. And then I might feel motivated to take a slap at them.

The latest issue contains an article by Ann Gauger, babbling about her recent publication disproving Darwinism, written with her colleague Douglas Axe, published in their tame ‘science’ journal, Bio-complexity, and edited by Michael Behe. It’s not work that could survive in a real journal, I’m afraid.

The work focuses on a diverse family of enzymes, the PLP-dependent transferases. These are all paralogs, or genes produced by duplication and divergence, as determined by their similar sequences. They picked two members of this family that use different substrates and catalyzed different reactions, and asked how they could possibly have evolved from each other…and they did it all wrong. The mistakes they made were fundamental, obvious, and amazingly stupid.

  • The cousin problem. You should have picked up on the key problem from my short description above: they picked two extant proteins and then asked how they could have evolved from each other. Imagine if I picked one of my many cousins — say, the tall, red-headed Mormon fellow from Oregon, or the slender fan of horses in California — and started enumerating our many differences and declared that I couldn’t possibly have evolved from either of them. You would rightly stop me and suggest that maybe my problem is that I didn’t evolve from my cousins — that maybe the smarter approach would be to look at our respective parents, and the grandparents we have in common, and trace the lines of descent.

    And you’d be right, of course. A more sensible way of looking at this problem is to start with a valid premise, and examine parental and grandparental states. Gauger and Axe don’t do that at all. They speculate about the huge number of possible intermediate states between two cousins, and decide that there are so many possibilities that the path from one to another is so improbable that it couldn’t have happened in the history of the planet. You might be able to say the same thing about me and my very different cousin, if you disregarded the fact that there actually were known intermediates.

  • The bridge hand problem. Creationists pull this one all the time. Here’s the situation: you are dealt 13 cards in a hand of bridge. What’s the probability that you’ll get the hand you’ve got? Obviously, the probability of getting a hand is 1.0, but the probability of getting any one specific arrangement of 13 cards is less than one in 635 billion. The silliness of the creationists is to point at a number like that and announce that the arrangement must have been designed. Gauger pulls this same stunt.

    …we calculate that the waiting time for a bacterial population to acquire seven specific mutations in a duplicated gene, none of which provide any functional benefit until all seven are present, is something like 1027 years. That’s a ten with 27 zeros after it. To put this in perspective, the age of the universe is believed to be on the order of 1010 years.

    If I played bridge very, very fast, dealing out one hand every minute, that means I’d still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 102 years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We’re here.

  • The talentless critic problem. Let’s pretend that the prior problems don’t exist (I know, that’s an awfully big hypothetical leap to make, but try). Let’s pretend therefore that the Gauger and Axe paper actually accomplishes what they claim: that neo-Darwinian mechanisms are inadequate to explain the origin of the family of PLP-dependent transferases. Now what? They’re here, obviously — how did they get here? They don’t say. They don’t even speculate; “intelligent design” is a phrase studiously avoided. Lord knows, their experiments and simulations aren’t even designed to reveal alternative mechanisms. This is their conclusion:

    …answers to the most interesting origins questions will probably remain elusive until the full range of explanatory alternatives is considered.

    Yeah, but…if Ann and Doug aren’t considering them in their papers, let alone putting together experiments to test them, why should I? And given that their protocols are so deeply flawed and built on faulty premises, I don’t think they’ve ruled out natural evolutionary mechanisms at all. I’ll be much more interested when they actually try to explore their unstated “explanatory alternatives” and show me a novel mechanism.

  • The much more attractive friend problem. I was surprised at one thing: usually creationists assiduously avoid the possibility of comparisons by, for instance, shutting off comments and not bothering to cite their critics, but in this case, Gauger actually links to a paper by Carroll*, Ortlund, and Thornton. It’s a terrible tactical mistake. Gauger and Axe are saying, “Ooh, we shit in a pot and we couldn’t even get mushrooms to grow in it,” and then pointing to the flourishing, hugely productive garden that Thornton has cultivated and saying, “…and they’re doing it all wrong.” It’s crazy. It just tells me my time is much better spent reading PLoS than Bio-complexity.

That other paper is so much better than the creationist paper, let’s talk about it.


*Sean Michael Carroll. No, not the physicist Sean M. Carroll who works at CalTech, and not the developmental biologist Sean B. Carroll at Madison, but another Sean Carroll at Harvard. It’s so confusing. If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

Suffer, Earthlings!

Creationists have this idea that history can be nothing but an unremitting decline — their version of the second law of thermodynamics is a weird thing that has everything ratcheting down into chaos equally, with no possibility of local decreases in entropy at the expense of an overall greater increase. They have almost convinced me. I once would have said no one could be dumber than Kent Hovind, but I have seen the works of his son Eric, and it’s a forthright demonstration of creationist thermodynamics.

Eric Hovind has disproven the K-T meteor theory of dinosaur extinction.

It’s impossible for a couple of reasons for an asteroid to kill them [dinosaurs], because the asteroid, they say, was millions of years ago. The earth isn’t millions of years old. And second, they’ve lived with man, as is very very evident.

I’m so sorry. I’m looking at that quote, and realizing that as soon as I press the “publish” button, it will sweep out in a wave of electrons all around the world, and trillions and trillions of innocent neurons will die in agony as they try to parse it. And I think, I have the power to do that, but do I have the right? Is it ethical to inflict such cognitive pain on so many people?

Eh. Atheist, scientist, slightly mad.

I press the button. Bwahahaha!

(Also on FtB)

Crazier than Ken Ham?

It’s hard to believe, but yes, there are Christians who are even worse than Ken Ham, and even more ignorant. Here’s one: Pastor Don Elmore of Union, Kentucky. He’s written a revealing screed against Answers in Genesis.

It starts gently enough, chatting about their rapid growth and praising AiG for their work against those wicked evolutionists. And then it goes off the rails.

I am aware of the forces supporting “Answers in Genesis”, these being the same powers that are supporting similar multi-cultural anti-Christian organizations such as Alpha, Promise Keepers, The Full Gospel Businessmen’s Association, Billy Graham ministries, producers of many modern Bible versions, and a multitude of other ministries. These forces are the anti-Christian powers seeking One World Government under man, not God. The essence of my criticism is to show that “Answers in Genesis” supports the humanistic and unbiblical “Brotherhood of Man” doctrine (which also is a Hindu/Roman Catholic/Masonic/Jewish/Judeo-Christian and World-Church belief).

Dang. He kinda hates everyone.

But what really has him worked up is miscegenation! These guys are really still around? The rest of this article is all angry rants about race mixing.

For instance, less than 60 years ago, mixed racial unions were illegal in most of the states in the United States and other White nations. But now, they are tolerated as being supposedly within God’s plan. Under the influence and promotion of the Jewish-Masonic-Papal-Communist/Socialist controlled governments and media, Western Christianity has succumbed to the approval of race mixing, and we will be looking at what is behind this. The Bible abounds with evidence of God’s clear will that the races be separate in every way. “Answers in Genesis” mould all its answers around Judeo-Christian doctrines and traditions, and claims a different basis and definition of “race” from that which the Bible gives. Furthermore, there is evidence of Jewish Talmudic sources, or of what the Apostle Paul calls “Jewish fables”.

That’s about as far as I could get without gagging. It wasn’t just the anti-semitism and the racism…it was that I was actually sympathizing with Answers in Genesis.

(Also on FtB)

I was wondering how you could have a Creation Evidence Expo

There was one in Indianopolis, and snarky people attended. I would think that at best they’d have a succession of people standing up at a lectern, looking shamefaced and confused before shrugging and sitting down with nothing to say, but apparently it went on for days.

This description of one speaker illuminates the process.

I have to say he did not disappoint. It really seemed to be two halves of non-related speeches spliced together. The first half of the speech was talking about how terrible American Society has become since 1963 when the Supreme Court ruled to take God out of schools. He began rambling statistics like unwed pregnancy in 10-14 year olds has gone up 553% since 1963 and violent crime up 998% or something like that. My jaw was on the floor and he didn’t bother to cite a source. The next half of his speech was about the Great Flood and how Pangaea split with the tower of Babel. He went on about how God gave all nations some sort of specialty and that’s why great scientist and geniuses come out of Europe. He was tracking the lineage of Peleg and Ham. Turns out Peleg isn’t related to Pele nor did he have a peg leg. Also, Ham’s offspring were not called bacon. He did let us know that AIDS came from having sex with monkeys and baboons. At least this year he didn’t blame AIDS on the gays.

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Now I understand. When you don’t have evidence, make some up.

I do like the image of plate tectonics explained by god smiting a tower in Mesopotamia and sending North America skittering westward to create the Atlantic Ocean. And the idea that Pangaea could be found on earth roughly, according to YEC chronology, in 600BCE is hilarious.

(Also on FtB)

Bob Enyart and Will Duffy, partners in idiocy

We’ve got another chittering weasel of a creationist raving in the comments, a fellow going by the name YesYouNeedJesus. He’s also sending me email.

PZ, I first heard about you on Bob Enyart’s radio show about the fact that you turned down an offer to debate Bob. I must say that my first impression of you is that you are smarter than most evolutionists. Smarter because the evolutionists that debate Bob get absolutely destroyed every time. Every evolutionist that I spoke to who was at the debate between Bob Enyart and Reasons to Believe willfully admitted that their side (evolution) lost. Bob’s debate with Eugenie Scott was just flat-out epic and is still my all-time favorite science debate. Of course they all made the mistake of debating Bob and you did not. You are smart, I’ll give you that. I think they made the mistake of underestimating Bob because he’s just a radio talk show host. Personally I think that Walt Brown is the greatest scientist of our day, but after Walt Brown, Bob is one of the most brilliant scientific minds I’ve ever listened to. I believe that the evolutionist’s new tactic is to avoid debating creationists because the arguments are just becoming impossible to refute. While that’s quite the tactical strategy and may work for a short time, it is encouraging to see the creation movement grow like a wildfire. And I do believe it’s just a short amount of time before we see evolution become the next ‘spontaneous generation’ and become obsolete. Don’t forget that if you dared question spontaneous generation, you were labeled as anti-science. Good luck to you. -Will

You read that, and apart from the creationist crazy, you get the impression that this guy is just someone with no ties to Enyart (other than his deep and abiding passionate love for him) who listened to the radio show, found out about these evilutionists, and ran over here to see what was up.

This is not the case. His name is Will Duffy, something revealed in the first few minutes of the video below, and he’s Bob Enyart’s producer.

You know, this kind of thing really bugs me. Why do you have to lie and mislead and conceal on the little, trivial things? Why hide the fact that you have a vested interest in Enyart’s show, and are actually deeply involved in the program? I see that, and right away, I know I’m dealing with a shameless liar for Jesus.

And then, of course, there’s the raving insanity. Walt Brown and Bob Enyart are the greatest scientists of the day? Someone alert the NAS and the Nobel Foundation!

Here’s the video. It’s a year old, and it’s a surprise to me (which goes to show how impressed I am with this Enyart freak). I dismissed a request to debate this kook — I’d just come off a debate with his loony pal, Jerry Bergman — and so he issued a challenge that I hadn’t even noticed until now.

He’s asking me to explain the origin of the superior oblique muscle, one of the extra-ocular muscles, which has a tendon that travels through a pulley-like strap called a trochlea. This muscle abducts and depresses the eye; try to look at your nose, and that’s one of the muscles responsible for pulling the eyeball in that direction. Enyart thinks the muscle would have been useless without the trochlear pulley, which is silly: the muscle could have had a different attachment in the orbit, or in the absence of the trochlea could have swiveled the eye upwards, or most likely of all, the suite of extra-ocular muscles and that little loop of tendon all co-evolved. We are well-integrated wholes, you know, and we didn’t evolve one toe at a time — nature selected for functionality as a complete organism.

OK, but Enyart has challenged me to explain how this feature evolved. I have an answer. It’s easy.

I don’t know.

I don’t see any obvious obstacle to an arrangement of muscles evolving, but I don’t know the details of this particular set. And there’s actually a very good reason for that.

This is a case where you have to step back from the creationist and look at the big picture. Don’t get bogged down in the details. Take a look at the whole context of the question.

We don’t know exactly how this evolved because all living vertebrates, with the exception of the lamprey, have the same arrangement of extra-ocular muscles. This is a primitive and very highly conserved condition, with no extant intermediates. We’ve seen the arrangement of these muscles in 400 million year old placoderm fossils, and they’re the same; these muscles probably evolved 450 million or more years ago, and we have no record of any intermediate state. So I don’t know, and neither does anyone else.

But that’s where we have to look at the big picture: Bob Enyart, a raving loon and young earth creationist who thinks the whole planet is less than 10,000 years old, is asking me to recount the details of an event that occurred almost half a billion years ago. I should think it’s enough to shatter his position and show that he’s wrong to simply note that however it evolved, it happened in animals 75,000 times older than he claims the planet is. Has he even noticed this little problem with his question?

I don’t think “one of the most brilliant minds” has.

Further, another of Will Duffy’s rants here has made a strange demand. Mary Schweitzer and Jack Horner identified some peculiar soft tissue deep in a T. rex bone, which Schweitzer claims is preserved collagen or fragments of blood vessels. This has been disputed, and some claim it’s scraps of a bacterial biofilm. But the main thing is that an unusual and difficult to identify material was found in a Cretaceous bone.

Will Duffy wants it carbon-dated. The fossil has already been dated; it’s over 70 million years old. Carbon dating is only good up to a maximum age of about 50,000 years. He wants to hold a yardstick up against a mile-long object and ask how long it is. This makes no sense at all.

Bob Enyart called Jack Horner and offered him $20,000 to measure the C14 in the T. rex specimen. You can tell Horner is both stunned and amused at the stupidity of the request.

The age of the specimen is not in question, and even if it were, carbon dating is so absurdly inappropriate and useless that only an ignorant clown would ask to do it: it doesn’t matter what number would come out of the measurement, it would be spurious, irrelevant, and uninterpretable…except that, because C14 does have an upper bound of 50,000 years, whatever number reported would be less than that, which is exactly what the creationists are trusting would happen. They’d love to hold that yardstick up against the mile long object and triumphantly announce that it’s only 36 inches long.

“Brilliant mind,” hah. That’s not a brain, it’s a dingleberry with pretensions.

(Also on FtB)

Andrew Brown has really put his foot in it this time

This is some unbelievably obtuse commentary on creationism from Andrew Brown. After noting that the proportion of creationists in the population is very large, and that many people will assent to the proposition that the earth is around 10,000 years old, he proceeds to place the blame.

This is quite clearly not a problem caused by religious belief. Even if we assume that all Muslims are creationists, and all Baptists, they would only be one in 10 of the self-reported creationists or young Earthers. What we have here is essentially a failure, on a quite staggering scale, of science and maths education. The people who think the Earth is 10,000 years old are essentially counting like the trolls in Terry Pratchett: “one, lots, many”. Ten thousand is to them a figure incalculably huge.

We’re to excuse religion when people dumbly parrot religious dogma? That number of 10,000 years isn’t just a random choice; it’s not arbitrary; it’s not a familiar, convenient, nice round number (why don’t they say it’s a million, or a billion, if it’s simply an ignorant guess?). Somehow, large numbers of people echo the specific claims of a narrow religious belief — a young earth, a worldwide flood, a six-day creation, and all that other foolishness — and somehow they just spontaneously, out of some peculiarly synchronistic ignorance, tend to give just these answers…and it’s not religion’s fault? This is an amazing example of plagiarized errors — if two students turned in exams with wrong answers that were identical to this degree, I’d nab ’em for cheating.

It also ignores the reality of the responses. It’s not just ignorance, I’ve seen that plenty of times, and usually when you teach a student something they didn’t know before, they react with please surprise — the lightbulb goes on above their heads. When I teach genetics or physiology, for instance, there’s hard stuff to master, but the students aren’t closed off to it: they’re signed up to learn it. Evolution is different. There are always some students who hear you tell them the earth is 4½ billion years old, we’re descended from other apes, we have fossils of intermediate forms — all wonderfully cool stuff that they should be thrilled to learn about — who resist and deny.

That’s the unique thing about evolution and a few other subjects. It’s not just that they’ve been in the dark about these controversies, it’s that they come into the classroom preloaded with dogma in opposition. Where does that problematic opposition come from?

Religion.

I really don’t mind and I certainly don’t belittle students who come in to the classroom unaware of the science they’re being taught — that’s the whole raison d’etre of having the classroom in the first place! What Brown is missing is the qualitatively different nature of the creationism argument: it’s an active and malicious anti-science promulgated in defense of religious myths. It clearly is a problem caused by religious belief.

(Also on FtB, and also Why Evolution is True and Butterflies & Wheels)

Fighting back against creationism

Creationism is not quite as pervasive a problem in the UK as it is in the US, but it’s still rising…so it’s good to see that British scientists are being aggressive in confronting bad educational policies. A number of prominent scientists, including Richard Dawkins and David Attenborough, have stepped forward to demand that evolution, not creationism, be taught in the classroom. Here is their position statement, with the signatories and organizations backing it:

Creationism and ‘intelligent design’

Creationism and ‘intelligent design’ are not scientific theories, but they are portrayed as scientific theories by some religious fundamentalists who attempt to have their views promoted in publicly-funded schools. There should be enforceable statutory guidance that they may not be presented as scientific theories in any publicly-funded school of whatever type.

Organisations like ‘Truth in Science’ are encouraging teachers to incorporate ‘intelligent design’ into their science teaching. ‘Truth in Science’ has sent free resources to all Secondary Heads of Science and to school librarians around the country that seek to undermine the theory of evolution and have ‘intelligent design’ ideas portrayed as credible scientific viewpoints. Speakers from Creation Ministries International are touring the UK, presenting themselves as scientists and their creationist views as science at a number of schools.

The current government guidance that creationism and ‘intelligent design’ should not be taught in school science should be made statutory and enforceable. It also needs to be made comprehensive so that it is clear that any portrayal of creationism and ‘intelligent design’ as science (whether it takes place in science lessons or not) is unacceptable.

Evolution

An understanding of evolution is central to understanding all aspects of biology. The teaching of evolution should be included at both primary and secondary levels in the National Curriculum and in all schools.

Currently, the study of evolution does not feature explicitly in the National Curriculum until year 10 (ages 14-15), but the government is overseeing a review of the whole curriculum with the revised National Curriculum for science being introduced in September 2012 to be made compulsory from 2013. Free Schools and Academies are not obliged to teach the National Curriculum and so are under no obligation to teach about evolution at all.

Excellent! When creationists underhandedly try to smuggle lies and nonsense into the classroom, it calls for a firm and uncompromising response.

Can we steal this and get a similar initiative going here in the US?

(Also on FtB)

My favorite creationist web page of all time

I just had to share. Look at this sample: at least 5 different fonts, 6 different colors, shadowed text, and all superimposed on an irrelevant and elaborate background.

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And then there’s the content: It’s a creation museum! It’s a taxidermy collection! And it’s run by some antique tools!

Savor the Creation Museum and Taxidermy Hall of Fame of North Carolina; I don’t think it will change any time in the near future, so there’s no hurry. It’s so nice of creationists to erect these monuments to stupidity and tastelessness on the web.

(Also on FtB)