Intelligent Design creationists unable to grapple with the substance. Surprise!

Uncommon Descent linked to my criticisms of the Biology of the Baroque, Intelligent Design creationism’s latest misconception, that biologists believe every detail of every organism is the product of natural selection…but they didn’t bother to quote any of my criticisms. It’s weird. They could have quoted the gist of my complaint:

So evolution should produce only the biological equivalent of sterile gray Soviet architecture, and if you find something that is the equivalent of a Baroque church, then evolution is refuted. This entire argument is built around what Michael Denton calls the fundamental assumption of Darwinism…that all novelties are adaptive. To which biologists around the world can only say, “Fu…wha?” in total confusion. That is not one of our assumptions at all. Novelties are going to arise as a product of chance mutation; if they are not maladaptive (and sometimes even if they are), they can spread through a population by chance-driven processes like drift. And some elaborate fripperies can acquire a selective advantage, like that example of Soviet architecture, the peacock’s tail, which this video actually uses as an example of non-adaptive order.

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Jonathan Wells is dead

Wells was one of the worst liars at the Discovery Institute, which is saying a lot. His pals out there in Seattle are writing his praises, of course; you won’t be surprised that they don’t understand why Wells’ books were loathed. Here’s Casey Luskin, who inevitably gets everything wrong.

A lot of people hated Jonathan, not because he was a hateworthy person, but because of the bad news he delivered about their scientific arguments. His ideas threatened their paradigm, and he wasn’t afraid to say so. But he didn’t hate back. He was a kind and caring person who used his gifts to make an immense impact, helping to reform junk science that had bloated evolution education worldwide. For all these reasons, Dr. Jonathan Wells will not be forgotten anytime soon. By his many friends, readers, and others who have benefited from his research, and of course by his loving family, he will be greatly missed.

He did not deliver bad news about scientific arguments; he didn’t understand, or pretended not to understand, the science he was criticizing. Everything he wrote was a misrepresentation. He didn’t reform junk science, he vomited up books that were nothing but junk science. I am confident that he wasn’t just ignorant, but that he intentionally, willfully, and maliciously lied about the science.

He was an intelligent man who got a Ph.D. in religious studies from Yale, and then got a second Ph.D. in cellular and developmental biology from the University of California Berkeley. There’s rarely ever a good reason to get a second Ph.D., and Wells had the worst reason ever: he had become a Moonie, and he got the second degree at the behest of his church so that he would be better equipped to destroy Darwinism.

Father’s [Rev. Moon’s] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.

Yeah, he was one of those misguided people who went through a research program not to learn anything, but to get a few letters after his name so he could pretend to be an authority. He also dishonored Berkeley with a badge of shame; it is appalling that someone so dishonest and so committed to distorting the science could fool the research scientists at that prestigious university.

He distorted every idea he touched. Larry Moran thoroughly debunked his treatment of junk DNA, for my part, I wrote about how he constantly botched and misinformed people about developmental biology. Here’s an example of one of my posts in which I wasted my time dissecting the glurge of garbage pouring out of his Moonie brain.

The next person–apparently a professor of developmental biology–objected that the film ignored facts showing the unity of life, especially the universality of the genetic code, the remarkable similarity of about 500 housekeeping genes in all living things, the role of HOX genes in building animal body plans, and the similarity of HOX genes in all animal phyla, including sponges. 1Steve began by pointing out that the genetic code is not universal, but the questioner loudly complained that 2he was not answering her questions. I stepped up and pointed out that housekeeping genes are similar in all living things because without them life is not possible. I acknowledged that HOX gene mutations can be quite dramatic (causing a fly to sprout legs from its head in place of antennae, for example), but 3HOX genes become active midway through development, 4long after the body plan is already established. 5They are also remarkably non-specific; for example, if a fly lacks a particular HOX gene and a comparable mouse HOX gene is inserted in its place, the fly develops normal fly parts, not mouse parts. Furthermore, 6the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: 7If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse? Finally, 8the presence of HOX genes in sponges (which, everyone agrees, appeared in the pre-Cambrian) still leaves unanswered the question of how such complex specified genes evolved in the first place.

The questioner became agitated and shouted out something to the effect that HOX gene duplication explained the increase in information needed for the diversification of animal body plans. 9I replied that duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content. She obviously wanted to continue the argument, but the moderator took the microphone to someone else.

It blows my mind, man, it blows my freakin’ mind. How can this guy really be this stupid? He has a Ph.D. from UC Berkeley in developmental biology, and he either really doesn’t understand basic ideas in the field, or he’s maliciously misrepresenting them…he’s lying to the audience. He’s describing how he so adroitly fielded questions from the audience, including this one from a professor of developmental biology, who was no doubt agitated by the fact that Wells was feeding the audience steaming balls of rancid horseshit. I can’t blame her. That was an awesomely dishonest/ignorant performance, and Wells is proud of himself. People should be angry at that fraud.

I’ve just pulled out this small, two-paragraph fragment from his longer post, because it’s about all I can bear. I’ve flagged a few things that I’ll explain — the Meyer/Wells tag team really is a pair of smug incompetents.

1The genetic code is universal, and is one of the pieces of evidence for common descent. There are a few variants in the natural world, but they are the exceptions that prove the rule: they are slightly modified versions of the original code that are derived by evolutionary processes. For instance, we can find examples of stop codons in mitochondria that have acquired an amino acid translation. You can read more about natural variation in the genetic code here.

2That’s right, he wasn’t answering her questions. Meyer was apparently bidding for time until the big fat liar next to him could get up a good head of steam.

3This implication that Hox gene expression is irrelevant because it is “late” was a staple of Wells’ book, Icons of Evolution and the Politically Incorrect Guide to Darwinism and Intelligent Design. It’s a sham. The phylotypic stage, when the Hox genes are exhibiting their standard patterns of expression, of humans is at 4-5 weeks (out of 40 weeks), and in zebrafish it’s at 18-24 hours. These are relatively early events. The major landmarks before this period are gastrulation, when major tissue layers are established, and neurulation, when the neural tube forms. Embryos are like elongate slugs with the beginnings of a few tissues before this time.

4What? Patterned Hox gene expression is associated with the establishment of the body plan. Prior to this time, all the embryonic chordate has of a body plan is a couple of specified axes, a notochord, and a dorsal nerve tube. The pharyngula stage/phylotypic stage is the time when Hox gene expression is ordered and active, when organogenesis is ongoing, and when the hallmarks of chordate embryology, like segmental myotomes, a tailbud, and branchial arches are forming.

5Hox genes are not non-specific. They have very specific patterning roles; you can’t substitute abdominal-B for labial, for instance. They can be artificially swapped between individuals of different phyla and still function, which ought, to a rational person, be regarded as evidence of common origin, but they definitely do instigate the assembly of different structures in different species, which is not at all surprising. When you put a mouse gene in a fly, you are transplanting one gene out of the many hundreds of developmental genes needed to build an eye; the eye that is assembled is built of 99% fly genes and 1% (and a very early, general 1%) mouse genes. If it did build a mouse eye in a fly, we’d have to throw out a lot of our understanding of molecular genetics and become Intelligent Design creationists.

Hox genes are initiators or selectors; they are not the embryonic structure itself. Think of it this way: the Hox genes just mark a region of the embryo and tell other genes to get to work. It’s as if you are contracting out the building of a house, and you stand before your subcontractors and tell them to build a wall at some particular place. If you’ve got a team of carpenters, they’ll build one kind of wall; masons will build a different kind.

6No, the similarity of Hox genes is not a problem. It’s an indicator of common descent. It’s evidence for evolution.

7Good god.

Why is a fly not a horse? Because Hox genes are not the blueprint, they are not the totality of developmental events that lead to the development of an organism. You might as well complain that the people building a tarpaper shack down by the railroad tracks are using hammers and nails, while the people building a MacMansion on the lakefront are also using hammers and nails, so shouldn’t their buildings come out the same? Somebody who said that would be universally regarded as a clueless moron. Ditto for a supposed developmental biologist who thinks horses and flies should come out the same because they both have Hox genes.

8You can find homeobox-containing genes in plants. All that sequence is is a common motif that has the property of binding DNA at particular nucleotide sequences. What makes for a Hox gene, specifically, is its organization into a regulated cluster. How such genes and gene clusters could arise is simply trivial in principle, although working out the specific historical details of how it happened is more complex and interesting.

The case of sponges is enlightening, because they show us an early step in the formation of the Hox cluster. Current thinking is that sponges don’t actually have a Hox cluster (the first true Hox genes evolved in cnidarians), they have a Hox-like cluster of what are called NK genes. Apparently, grouping a set of transcription factors into a complex isn’t that uncommon in evolution.

9If you photocopy a paper, the paper doesn’t acquire more information. But if you’ve got two identical twins, A who is holding one copy of the paper, and B who is holding two copies of the same paper, B has somewhat more information. Wells’ analogy is a patent red herring.

The ancestral cnidarian proto-Hox cluster is thought to have contained four Hox genes. Humans have 39 Hox genes organized into four clusters. Which taxon contains more information in its Hox clusters? This is a trick question for Wells; people with normal intelligence, like most of you readers, would have no problem recognizing that 39 is a bigger number than 4. Jonathan Wells seems to have missed that day in his first grade arithmetic class.

It still infuriates me that a guy with a Ph.D. in developmental biology from Berkely would ask, if flies have HOX genes similar to those in a horse, why is a fly not a horse? Because the Hox genes only trigger the deployment of downstream genes of the animal, ya idjit.

Casey Luskin is wrong. I didn’t hate Wells personally — I never met him — but I did hate his lies, of which there were many, whole books worth of ’em. Good riddance to lying scum.

It’s always a good time to be an atheist

The Intelligent Design creationists had a discombobulating conversation that they thought was brilliant, but just left me wondering what planet they live on. They were discussing when it was a better time to be an atheist, and apparently it was in 1890, when being an atheist would prohibit you from entering a major university.

Jay Richards: The fact that we now talk about the universe as having an age is a significant update from a century and a half ago. It leads to new questions. Is it unique? Was there one beginning? Can we talk about the beginning? But that’s a different sort of situation. And so, I think if you’re thinking in terms of worldviews, I would much rather be a materialist where everyone assumed the universe was eternal than be at a moment in which virtually everyone, whether skeptic or believer, says, “Well, the universe has an age, so it’s got a finite past.”

Peter Robinson: You’d rather be a materialist in the 1890s…

Jay Richards: Exactly.

Peter Robinson: Than today?

Jay Richards: Yes, and I think it’s much easier to be a theist when standard cosmology says “Well, the universe hasn’t always been here.” It’s no longer a good candidate for an ultimate explanation if it had a beginning.

Jay Richards is not an atheist, of course, which makes one wonder about his ability to see the world from the perspective of an atheist. But OK, he considers himself an authority on the godless. That does not surprise me at all.

As an atheist and a materialist, though, I can say pretty definitely that the better time to be a materialist is when we have more information about the material world, which ought to be obvious. The big difference between scientists and the clowns at the Discovery Institute is that we welcome new information and aren’t trying to force-fit the universe into a mold decided upon by ancient civilizations.

So our universe had a beginning? We happily filed that data away with all the other facts about the material nature of the world. There’s nothing in that observation that implies a supernatural or magical origin — in fact, to the contrary, what led to that conclusion is physical observation and measurement, and physicists, not theologians, are exploring the 13.8 billion years of its existence.

News for Jay Richards: the Big Bang is not evidence for Jesus. It’s a bad time to be a theist when your god is getting squeezed into smaller and smaller gaps, and godless science is doing a better job of explaining how the world works than your holy book.

Uh-oh — I don’t think the metaphor works

This cartoon does sort of accurately illustrate how Muller’s Ratchet works, but like any metaphor, it drags in a lot of baggage.

Here’s what I don’t like: every step involves intent. In the metaphor, every change has a purpose and brings in a functional element in addition to the random noise and degradation, and the recombination step is portrayed as combining specific, useful parts. Intelligent design creationists will love this cartoon, which is too bad.

I guess my primary objection is that last panel that says “…if you have an image editor that lets you spice together parts of two images, you can make a new version with the best parts of both“. Recombination doesn’t discriminate what parts are best. It’s random.

Gussying up creationism with math doesn’t make it valid

I’m trying to read this article, “Using statistical methods to model the fine-tuning of molecular machines and systems” by Thorvaldsen and Hössjer, and wondering why I even bother, and why the Journal of Theoretical Biology bothered to publish it, because a) it undermines its own premise in the introduction, b) it’s loaded with irrelevant math, c) it contains no observations or experiments, and d) at the end it devolves into the usual circle jerk of references to the usual suspects in the Intelligent Design community. I had to throw up my hands and give up. It’s just mathematicians juggling assumptions and numbers to come to the conclusion they want.

The one interesting aspect is that unlike the Discovery Institute gang, they do give clear explanations of what they mean by “design” and “fine tuning” — it’s just that, once you read them, you feel like telling them that their work is done, further noodling about is pointless. Maybe that’s why the Intelligent Design creationists try harder to fog over the meaning of the words they use?

Anyway, here’s the only interesting stuff in the whole thing.

The term fine-tuning is used to characterize sensitive dependences of functions or properties on the values of certain parameters (cf. Friederich, 2018). While technological devices are fine-tuned products of actual engineers and manufacturers who designed and built them, only sensitivity with respect to the values of certain parameters or initial conditions are considered sufficient in the present paper. We define fine-tuning as an object with two properties: it must a) be unlikely to have occurred by chance, under the relevant probability distribution (i.e. complex), and b) conform to an independent or detached specification (i.e. specific).

To which I would reply that a) unlikely events happen all the time, so mere measures of probability, especially after the fact, are of little consequence, and b) groovy, so does this mean you are going to provide an independent or detached specification for a specific evolutionary event? [Answer: No, they are not.] If your definition requires addressing two parameters, and at the very outset of your project you have to admit that you don’t have the second one and that playing mathematical games cannot provide it, then aren’t we done? That was the second paragraph of the whole article, which makes for a quick read, too.

But no, sorry, they go on.

The notion of design is also widely used within both historic and contemporary science (Thorvaldsen and Øhrstrøm, 2013). The concept will need a description for its use in our setting. A design is a specification or plan for the construction of an object or system, or the result of that specification or plan in the form of a product.

Yes, yes. I’ve been saying this for years. If you want to claim there was a design for an organism, show me the blueprint from which it was built, and I’ll believe you. If you go to Mars and find a set of billion year old program specifications for Project Mouse, laid out by the Martian designers, with a couple of thousand manuals that lay out the details of the biochemistry, physiology, and morphology of Mus musculus, then I’ll have to admit that you’ve got solid evidence that mice are the product of design. You’ve said it right there in your definition, that you have to have a specification or plan the precedes the product.

Except then they immediately waffle. All you need is the product itself, and then you get to infer the specification or plan. That makes no sense. I can find a pebble in my yard which is unique in all of its particulars, where every scrape and mark and fracture sets it apart from otherwise similar pebbles. The probability of that specific pebble having its specific constellation of attributes is minuscule. Are you going to try and tell me that therefore there is somewhere on file in the Great Designer’s filing cabinet a project laid out for Pebble, Minnesota, 21st Century, Myers yard, grey, roughly ovoid? You might believe that’s the case, but I’d like to see it.

Instead, we get a lesson in etymology. I had to laugh, this is so ridiculously irrelevant.

The very term design is from the Medieval Latin word “designare” (denoting “mark out, point out, choose”); from “de” (out) and “signum” (identifying mark, sign). Hence, a public notice that advertises something or gives information.

Great. So where’s the public notice? Somewhere in the main Megabrantis office which is open on Tuesdays, between 1 and 1:15pm, standard Vogsphere time?

The design usually has to satisfy certain goals and constraints. It is also expected to interact with a certain environment, and thus be realized in the physical world. Humans have a powerful intuitive understanding of design that precedes modern science. Our common intuitions invariably begin with recognizing a pattern as a mark of design. The problem has been that our intuitions about design have been unrefined and pre-theoretical. For this reason, it is relevant to ask ourselves whether it is possible to turn the tables on this disparity and place those rough and pre-theoretical intuitions on a firm scientific foundation.

Just once, please consider that our intuitions can be wrong, rather than struggling to find some mathematical justification for them.

Unfortunately, the paper is primarily about fine tuning, allowing them to ignore this problem, and they’re going to move on.

Fine-tuning and design are related entities. Fine-tuning is a bottom-up method, while design is more like a top-down approach. Hence, we focus on the topic of fine-tuning in the present paper and address the following questions: Is it possible to recognize fine-tuning in biological systems at the levels of functional proteins, protein groups and cellular networks? Can fine-tuning in molecular biology be formulated using state of the art statistical methods, or are the arguments just “in the eyes of the beholder”?

Yes. We are quite confident that biological organisms have been fine tuned by natural selection. Is that what you mean?

There’s no point in worrying about it, though, because after I read the following sentence I threw my hard copy of the paper in the trash.

The chances that the universe should be life permitting are so infinitesimal as to be incomprehensible and incalculable.

But…but…if they’re incalculable, then how did you determine that they are infinitesimal? Jesus. Creationist mathematicians.

When will the criticisms of evolutionary psychology sink in?

I’ve been complaining for years, as have others. The defenders of evolutionary psychology just carry on, doing more and more garbage science built on ignorance of evolutionary biology, publishing the same ol’ crap to pollute the scientific literature. It’s embarrassing.

Now Subrena Smith tries valiantly to penetrate their crania. It’s a familiar explanation. She sees it as a matching problem between their claims about the structure of the brain and behavioral history.

The architecture of the modern mind might resemble that of early humans without this architecture having being selected for and genetically transmitted through the generations. Evolutionary psychological claims, therefore, fail unless practitioners can show that mental structures underpinning present-day behaviors are structures that evolved in prehistory for the performance of adaptive tasks that it is still their function to perform. This is the matching problem.

In a little more detail…

Ancestral and present-day psychological structures have to match in the way that is needed for evolutionary psychological inferences to succeed. For this, three conditions must be met. First, determine that the function of some contemporary mechanism is the one that an ancestral mechanism was selected for performing. Next, determine that the contemporary mechanism has the same function as the ancestral one because of its being descended from the ancestral mechanism. Finally, determine which ancestral mechanisms are related to which contemporary ones in this way.

It’s not sufficient to assume that the required identities are obvious. They need to be demonstrated. Solving the matching problem requires knowing about the psychological architecture of our prehistoric ancestors. But it is difficult to see how this knowledge can possibly be acquired. We do not, and very probably cannot, know much about the prehistoric human mind. Some evolutionary psychologists dispute this. They argue that although we do not have access to these individuals’ minds, we can “read off” ancestral mechanisms from the adaptive challenges that they faced. For example, because predator-evasion was an adaptive challenge, natural selection must have installed a predator-evasion mechanism. This inferential strategy works only if all mental structures are adaptations, if adaptationist explanations are difficult to come by, and if adaptations are easily characterized. There is no reason to assume that all mental structures are adaptations, just as there is no reason to assume that all traits are adaptations. We also know that adaptationist hypotheses are easy to come by. And finally, there is the problem of how to characterize traits. Any adaptive problem characterized in a coarse-grained way (for example, “predator evasion”) can equally be characterized as an aggregate of finer-grained problems. And these can, in turn, be characterized as an aggregate for even finer-grained problems. This introduces indeterminacy and arbitrariness into how adaptive challenges are to be characterized, and therefore, what mental structures are hypothesized to be responses to those challenges. This difficulty raises an additional obstacle for resolving the matching problem. If there is no fact of the matter about how psychological mechanisms are to be individuated, then there is no fact of the matter about how they are to be matched.

One problem is that evolutionary psychologists all seem to think that their assumptions are obvious — and if you don’t agree, why, you must truly hate Charles Darwin and be little better than a creationist. Man, it’s weird when the intelligent design creationists are all calling you a dogmatic Darwinist, and the evolutionary psychologists are accusing you of being an intelligent design creationist. They’re both wrong.

Phillip Johnson is dead

The last time I talked about Phillip Johnson it was to say I am honestly happy that Phillip Johnson is still alive — I wanted him to witness the ignominious decline of his baby, Intelligent Design creationism, and live to suffer with it’s irrelevancy and routine rejection and abysmal failure to challenge science at all. I said then:

I make no bones about the fact that I consider Johnson to be an intellectual criminal.

The reason is simple: Jason Rosenhouse is right. Intelligent Design is dead. I want Johnson to suffer the pain and frustration of knowing that he has wasted his life, and that he’ll be remembered as a failure.

His book was a cobbled together hodge-podge of specious reasoning, using legal logic to raise unwarranted doubts over concepts he couldn’t understand. He was no scientist; neither are his followers. He was a pettifogging lawyer coming off a divorce and a midlife crisis who tried to find redemption by lying for Jesus. It didn’t work.

I guess, then, I should now be sad that Johnson has joined his movement. Phillip Johnson is dead, but I’m not. I don’t care. He died as Intelligent Design did, barely remarked, recognized mainly by his cult sympathizers and the people who fought against his nonsense. We’ll just remember, as Larry Moran said, that Johnson was the very best of the Intelligent Design creationists.

Shades of Paul Nelson!

Wow, this is so familiar. Jeff Shallit, who studies information theory, asked a simple question of those intelligent design creationists who love to pretend information theory is on their side.

Five years ago, the illustrious Baylor professor Robert Marks II made the following claim: “we all agree that a picture of Mount Rushmore with the busts of four US Presidents contains more information than a picture of Mount Fuji”.

I didn’t agree, so I asked the illustrious Marks for a calculation or other rationale supporting this claim.

After three months, no reply. So I asked again.

Can you guess what their answer was, can you, huh? No prizes if you guess correctly though, because this is way too easy.

I’ve been saying this for decades!

As Matthew Herron points out,

The intelligent design blogs I read, when they’re not busy vilifying “Darwinists”, spend much of their time extolling the super-duper complexity of life, but here’s the thing: no one is arguing that life isn’t complex. To my knowledge, no biologist has ever argued that, and if they have, they’re wrong. As Strassmann and Queller point out, Darwin and Paley both proposed explanations for complexity, and one of those explanations turned out to be right. As much as its advocates want it to be, complexity is not evidence for intelligent design.

When Intelligent Design creationists play at being scientists (Hi, Stephen Meyer, you boring fraud you), this is all they do, parrot articles that explain the bewildering complexity of the cell, as if that means it must have been designed. That’s all Behe does, is natter on about how complicated biology is, and then make an unfounded leap from “it’s too complex for me to understand” to “therefore, the god who designed it must be really smart”, not addressing the issue at hand…was it designed at all?

Then all of their fans chime in at any criticism of the ID argument with repetitions of the “It’s really complex” claim, which is totally fucking irrelevant. It seems to impress the rubes, though.