Studying all the time? Quit before your brain develops a saddle shape from the sheer weight of your learning. Take a break and have some fun.

Here are some cartoons in the intelligent design controversy. Oh, and an entire site of spoofs, sendups, and jokes, courtesy of The Brites organization, directed (to a very slight extent) by Dr. Galapagos ("Gloppy") Finch, a loopy scientist who may or may not be a bird in actual fact.

And so what? Some of those gray parrots are smarter than me, but, like, I pay for the birdseed around here, so ...

Also: Oh, and let's not forget How died the dinosaur? Everyone has a shovel in the grave, it seems.

Or perhaps one should ask, how did butterflies start to become caterpillars?

Some life forms go through stages that bear no resemblance to each other. The caterpillar, for example, bears little resemblance to the butterfly that it becomes. How did that process evolve?

Recently, two scientists suggested that perhaps the genomes of two species could somehow fuse. The Origins of Larvae, a recent article by Donald I. Williamson and Sonya E. Vickers in American Scientist (November-December 2007), advances the possibility that "mismatches between the forms of adult animals and their larvae may reflect fused genomes, expressed in sequence in complex life histories." Fused genomes is a fairly radical idea, as the abstract admits:

Larvae, the immature forms of many animals, are distinct from adult forms by definition. In many life histories—caterpillars and the trochophore larvae of clams and sea snails are examples—larvae and adults bear no resemblance to each other. Biologist Williamson has proposed that larvae are juvenile forms acquired through hybridization—the fusing of two genomes, one of which is now expressed early in an animal's life, the other late. This hypothesis, which goes against traditional thinking that branches on the evolutionary tree cannot fuse to form chimeric species, is one of several possible solutions to open questions about the evolution of larvae. Although an experiment did not yield convincing DNA evidence, the hypothesis is consistent with certain patterns seen in the distribution of genes across species. Along with other evidence of cross-species hybridization, it implies a pattern of evolution that looks more like a network than like Darwin's tree of life.

In other words, the question is so far from being resolved in conventional thinking about evolution that these researchers contemplate replacing Darwin's "tree of life" - the governing paradigm - with a network. And they suggest this even though an experiment to detect fused genomes "did not yield convincing DNA evidence."

To understand why some scientists suggest radical theories like fused genomes, let's look at some other available explanations. Evowiki, for example, offers several Darwinian explanations:

- Many insects undergo fewer stages of metamorphosis than butterflies do. True enough, but the radical transformations of butterfly metamorphosis are not really accounted for by observing that many insects do not undergo them. In fact, it makes the question even more of a puzzle.

- Also, caterpillars are said to be "precocious embryos" that hatched before they assumed the adult form. But how did the original "precocious embryos" survive, when early hatching usually means early death. Also, was there ever a point at which butterflies emerged fully formed from the egg?

- Another attempted explanation is that a larval stage evolved because the species as a whole benefits from the fact that the adults and larva are not in competition. For example, caterpillars and butterflies are not in competition with each other for food because, generally, caterpillars eat leaves and butterflies drink nectar. Thus, the existence of a huge number of caterpillars - who do not reproduce while in that stage - does not threaten the food supply of butterflies, who do reproduce. However, explaining why a given change may be a benefit does not tell us how it happened. It helps us understand why the species did not go extinct as a result of the change.

Part of the problem is that we do not have a fossil record for the details of how butterflies got started. This area is so far from being understood that it prompts radical theories.

This article helps us understand the scope of the adaptations to be explained, and it's only about how butterfly wing scales can be an efficient three-layered mirror.

2006 and 2007 have been years in which a number of key science papers addressed things we know - that ain't so. For example, there have been serious challenges to the long contested "molecular clock" theory. The theory - which has been around since the 1960s - is that molecular data based on assumed rates of Darwinian evolution can be used to reconstruct evolutionary relationships. As an article on the University of Maryland Department of Geology site puts it,

A molecular clock is a gene or protein common in the cells of all living things, from bacteria to plants to animals. According to some researchers, these molecules change, or mutate with clock-like regularity. Over geological time mutations begin to build up within the molecular clocks of different animal groups, or phyla, once they split off from a common ancestor. Scientists calibrate the speed of these genetic clocks by counting up the number of mutations that have accumulated over a known interval of time, in specific groups of modern fish; skeletons of the earliest fish are well preserved in rocks that have already been dated using geological clocks. Thus by knowing the speed of the molecular clock, researchers need only count up the number of genetic mutations in a wide range of animal groups to project back to the time, before there were fossils, when each phyla evolved.

In other words, we could run the clock backward and find out what happened in the history of life. In that case, we should expect to find that the fossil record and the molecular data match. The problem is that they often don't match. In one example,

Foote's team chose to analyse placental mammals (the group of mammals that produce live young nurtured through a placenta in the mothers womb - including humans, bats, whales, elephants and mice). Fossil evidence suggests placental mammals first appeared on Earth some 65 million years ago while the biochemical data suggests a date of 130 million years. The team asked the question: "Is the fossil record so poor that the group could have been undetected for 65 million years?" - "Fossils cast doubt on molecular clock" News in Science (February 26, 1999)

They don't think so. They argue, based on evidence, that the fossil record is fine and the clock is not. In the science literature, many adjustments are offered to make the fossil record and molecular data match. Of course, some adjustment is certainly inevitable, but after a while a question arises. One can live with a clock that is routinely ten minutes slow. But if it is variably slow, slower at some times than others, there may come a point when one asks, why consult a clock anyway? Or, more to the point, should this device properly be called a clock? The clock may not have run at all, according to a 2006 paper by Jeffrey H. Schwartz and Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," in the journal Biological Theory.

The abstract of the Schwartz and Maresca paper reads:

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”

Addressing the fallout, British physicist David Tyler commented earlier this year,

The first part of the paper addresses historical aspects of "molecular systematics" to better understand the "theoretical and methodological underpinnings." The authors are concerned to find out "how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology." This they do with an incisiveness rarely appearing on the printed page of refereed journals. The MA (molecular assumption) is acknowledged to be dominant but to rest on theoretical rather than empirical foundations. "No doubt because it was completely Darwinian, the MA continued to dominate the increasingly influential field of what was now often called molecular systematics." [ ... ] It has been a major problem for Darwinism that its foundations are regarded as inviolable and a 'given'. "Our review [...] reveals that, no matter how sophisticated their mathematical models, molecular systematists have not questioned the basic assumptions upon which they are based. Thus, while refining computer programs to analyze molecular data phylogenetically continues apace [...] with statements of certitude about results following suit, no algorithm is more viable than the assumptions that inform it." The authors offer the hope that their critical review will open the way for a more integrated approach to systematics. This is a paper that will disturb the Darwinists, but it will offer encouragement to all who want to see less ideology in evolutionary thinking and who want to follow the evidence wherever it leads.

There's also this December 2006 paper, "Dates from the molecular clock: how wrong can we be?" by Mário J F Pulquério and Richard A Nichols in Trends in Ecology and Evolution, which makes a similar point,

Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

Actually, challenges to the molecular clock are not new. In 1990, Michael Behe published a paper in Trends in Biochemical Science, "Histone deletion mutants challenge the molecular clock hypothesis"(15: 374-376) on the subject, and uncertainty and adjustments are regularly acknowledged in professional sources.

But information in the school system may portray much more certainty than the science literature allows. For example, here's information on the molecular clock destined for the school system (notice the advertisement for lesson plans). Also, notice how much more certain Berkeley's Evolution 101 sounds than the scientists do.

Stephen Jay Gould, the great American paleontologist, liked to say - particularly in A Wonderful Life, that if the tape of evolution were replayed a million times, a species like ours would not necessarily evolve. A debate rages to this day about whether Gould meant chance, as Daniel Dennett claims, or contingency, as Michael Shermer claims.

Biochemist Michael Denton of the University of Otago in New Zealand has an interesting take on the more critical question of what would happen in any case, in Nature's Destiny. He writes,

Curiously, the evolution tape has been played again, at least in part. This has occurred on several occasions.

Citing the fact that South America and Australia were isolated from the other continents for the better part of 60 million years, he discusses the marsupials (mammals like kangaroos that nurture their young in a pouch on the abdomen rather than a uterus inside the female's body):

The diversification of the marsupials in Australia is very instructive. Almost every type of placental mammal has its counterpart among the marsupials. There is a marsupial lion, cat, wolf, mole, anteater, jerboa, and flying squirrel. There was even a giant wombat equivalent to the placental rhino. (Denton, Nature's Destiny, 287)

He concedes the uniqueness of the kangaroo (a giant jumping rat), but notes that

The skull of the marsupial wolf is amazingly similar to that of the placental wolf.

, a fact discussed and illustrated in The Design of Life (115-16). He notes a similar pattern in South America, and says, "parallelism and long-term evolutionary trends have always struck many biologists, especially paleontologists as difficult to account for in terms of undirected Darwinian models of evolution." (Denton, 288) Denton is not a design theorist, but more of a determinist - that is, he thinks that some events occur in nature because they are constrained by mechanisms that are not yet known. Would the marsupials ever have produced creatures equivalent to modern humans? That's hard to know, because modern humans are very recent in the history of Earth (200 000 years ago at best) and we spread around the globe, including Australia.

It seems like the marsupials never got the chance to try.

In an online note to his recent book, Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body Author Neil Shubin, who directed the anatomy course at the Univrsity of Chicago Medical school, writes,

It turns out that being a paleontologist is a huge advantage in teaching human anatomy. Why? The best roadmaps to human bodies lie in the bodies of other animals. The simplest way to teach students the nerves in the human head is to show them the state of affairs in sharks. The easiest roadmap to their limbs lies in fish. Reptiles are a real help with the structure of the brain. The reason is that the bodies of these creatures are simpler versions of ours.

The focus of Shubin's original study was Tiktaalik, a 375-million-year-old fish discovered in 2004 in the Canadian Arctic (also called "fishapod"). This early fish had a functional neck, eyes in the top of its head, and front fins that were strong enough to function somewhat like feet, propping up its body, wqhih suggests that it was developing along the lines of an amphibians. Amphibians, such as frogs and toads, live their adult lives on land but their early lives in water, as did most early life forms. Amphibians are considered to be the earliest vertebrates (animals with backbones). Tiktaalik helps illustrate the difference between the approach of scientists who are convinced Darwinists and that of scientists who view the problems of evolution primarily in terms of information theory (intelligent design). The Darwinist says, There! - we have found a missing link, so now we KNOW! what happened. For example, from the Time Magazine article about "fishapod"), we learn, regarding Tiktaalik's front fin,

On land, observes Shubin's collaborator Ted Daeschler, chair of vertebrate zoology at Philadelphia's Academy of Natural Sciences, such an appendage would have been worse than useless. But it would have been more than adequate for propping the animal's head above the water so that it could survey its surroundings or for anchoring it underwater as it waited to ambush its prey. The advantage of being able to gulp air through lungs as well as gills would likewise have been immediate, given that the fishapod made its home in warm, shallow waters that were frequently rendered inhospitable by decaying vegetation.

Actually, we do not know whether any of that happened. Ted Daeschler assumes that Darwinian evolution (natural selection acting on random mutation) somehow produced these changes. Thus, picking and choosing among the environment conditions that we also assume to have existed, we construct a story about how it happened without any specific evidence.

The information theorist I consulted had an entirely different approach to the problem. He said that we do not know what happened, because we do not know how the information that produced this change came to be in the system. We have observed only the change itself, not the arrival of the information. The problem, he said, is not with the changes that are required to produce an amphibian but with determining exactly how such changes came about:

There are two ways to look at the problem in going from fish to Tiktaalik and then from Tiktaalik to amphibian. If we merely look at a body plan then it doesn't take too much imagination to say that the fish evolved into Tiktaalik and then the Tiktaalik evolved into the amphibian through natural selection. That is a very crude way of looking at evolution, however .... very 19th centuryish.

It's kind of like looking at a laptop computer and a pizza box ... there are similarities in structure and an argument could be made (provided one did not open either the laptop or the pizza box) that natural processes had turned the pizza box into a shape of a laptop. The other approach (more appropriate to the 21st century) is to look at the coding changes in the genome that would be required to go from a fish to Tiktaalik and from Tiktaalik to an amphibian.

It never ceases to amaze me that Darwinists can so blithely create a scenario based on morphology and not so much as breath one sentence about the massive coding changes that would be required. Have they no concept of 21st century information requirements? Of course it is true that we do not have the DNA of Tiktaalik, but we do have DNA for Coelecanth and for amphibians. Decent science would require, at the very least, a careful analysis of the coding difference between Coelecanth and some representative amphibian before a scientist would go out on a limb and announce that the evolutionary change (without any ID input) is even feasible, let alone represented by Tiktaalik.

One reason why the intelligent design controversy is intractable is that many scientists are stuck in the primitive mode of discovering that a change occurred and declaring that "Darwin's theory explains this!" They then make up stories to show how Darwin's theory could explain it.

You know the sort of thing: "Tiktaalik survived by propping itself up and eating small fish in shallow waters." Maybe Tiktaalik did that. But that does not explain how he found himself to be in any position to do it.

That kind of just-so story will not wash any more, because the enormous inner complexity of the design of life forms requires a more detailed accounting than that.

Darwin's theory is simply not adequate to the task, and the resources spent propping it up would be better used otherwise.

"Now if you talk about evidence of design in physics or cosmology, you are put under the category of intelligent design, and you are immediately labeled a fundamentalist or worse."

- Guillermo Gonzalez

Iowa State University astronomer Guillermo Gonzalez has made the news a few times recently, but not primarily for his accomplishments in the study of stars orbited by planets (exoplanets).

And not for his popular book and DVD, Privileged Planet, with philosopher Jay Richards, in which he says  that Earth is remarkably well suited to exploration of the solar system and the galaxy. Our position between spiral arms of the galaxy* enables us to see into the Milky Way in such a way that excess starlight does not occlude our view. 

Or even for his emphasis on the relationship between the size of the moon and the sun: The moon exactly covers the sun during a total solar eclipse, enabling astronomers like himself to garner priceless data.

Gonzalez has called his view - that Earth's position in the universe was designed in such a way that we can explore it - a "privileged planet" hypothesis - hence the name of the book.

These are not new ideas in themselves. Similar ideas have been explored in Peter Ward and Donald Brownlee's Rare Earth: Why Complex Life Is Uncommon in the Universe.

However, the showing of the Privileged Planet film at the Smithsonian amid much controversy in June 2005 probably drew unfavourable attention to Gonzalez, as did the popular book and DVD themselves. The Smithsonian was the late Carl Sagan's territory, and it must be said that Privileged Planet explicitly denies the doctrine of St. Carl and all his faithful followers, that Earth is merely a pale blue dot lost in the cosmos.

Not even close, says Gonzalez; we could not be better placed if we had hired consultants. Possibly worse.

No, Gonzalez is best known for being denied tenure in May 2007 at ISU on account of his sympathies with intelligent design. The recent disclosure of the e-mail trail made clear that his sympathies with intelligent design were the reason for the denial, though some claim that he had also failed unwritten rules.

Actually, he had been a target for some time before he was officially denied. I interviewed Gonzalez recently by phone from his home in Iowa:

O'Leary: Dr. Gonzalez, you are described as a supporter of intelligent design. In your case that seems to mean intelligent design of the universe in general, not of life forms in particular. Is that right?

Gonzalez: That's right - intelligent design specifically with regard to my specialty - but that also means that I support ID research by others, but I don't participate in it.

O'Leary: Is your "privileged planet" hypothesis in some sense a subset of the fine tuning hypothesis - that the universe seems as if it were designed for life to come into existence?

Gonzalez: I would say it’s related. It includes the fine tuning of the universe for life, but also for discovery. Fine tuning in physics points to a purpose - the presence of life in the universe. But, further than that, it points to a purpose of life - to do science, to do discovery.

O'Leary: Why would scientists be opposed to that?

Gonzalez: In our book we say that the discovery that the universe is designed for discovery shows that science was built into the universe from the beginning. I’ve been surprised by the strong opposition. The answer is frankly political. I have got caught up in this debate over ID including all kinds of things I have nothing to do with, like whether ID should be taught in public schools. The reasons many scientists give [for opposition] have nothing do to with our thesis. The problem comes from where the debate has devolved over the years - it has become very nasty - for many years, biological evolution was separate from the debate over cosmic design.

O'Leary: Has the debate over fine tuning changed?

Gonzalez: Now if you talk about evidence of design in physics or cosmology, you are put under the category of intelligent design, and you are immediately labeled a fundamentalist or worse.

O'Leary: When I first covered the story about the showing of the Privileged Planet DVD at the Smithsonian, the New York Times reporter stated that the film was “anti-evolution” (he had not seen the film, which explains cosmological evolution and does not address biological evolution). Did the perception that you might be anti-evolution in some ideological sense contribute to a climate of distrust about you?

Gonzalez: Yes, there was no question that there was a tactic to brand me as anti-evolution. The petition against me was first circulated in email at my university's biology department. It had nothing to do with my privileged planet thesis. No one in physics or astronomy signed but there were over 100 signatories in philosophy, biology, earth sciences, and atmospheric science.

O'Leary: Ann Applebaum of the Washington Post claimed that Privileged Planet was a “religious” film. Can you comment on that?

Gonzalez: I spoke to her. It's not religious and it's not creationism. It was like talking to a wall, like talking to a post ...

O'Leary: I have noticed in the popular science media, a huge, almost obsessive interest in the idea that there are many universes and that therefore ours only accidentally works. How seriously is this idea taken by professional astronomers and for what reasons?

Gonzalez: There is a mix of views among physicists, astronomers, and cosmologists. Accredited scientists generally are mostly very skeptical, and many don't even view it as science. You can never test the idea. I've had many conversations with colleagues who are very skeptical You see it brought up frequently in pop science journals and preprints. Among practical scientists in one- on-one discussion - they say that stuff is pure speculation! Yet it is taken very seriously in popular science magazines.

Gonzalez has appealed to the Board of Regents of Iowa, in his tenure case. Beyond that, he is an astronomer looking for a job with people who can tolerate the idea that the universe might show evidence of design and Earth might be positioned for exploration. Captain Picard of Star Trek would love him, I am sure.

* Correction: Originally, the posts had said "on" a spiral arm, but Guillermo Gonzalez has kindly written me to say that my notes are in error. We are between spiral arms.

In an op-ed piece in the Philadelphia Inquirer (November 21, 2005), Guillermo Gonzalez and his Privileged Planet co-author Jay Richards addressed the claim that intelligent design was both unfalsifiable and falsified:

ID is said to be unscientific because it is supposedly unfalsifiable or untestable: Nothing can count against it. Some critics even claim, in the same breath, both that ID is unfalsifiable and that it has been falsified. We recently received a set of questions from a reporter doing a story on ID. One question asked how we dealt with the fact that intelligent design was unfalsifiable. Another asked for our response to biologist Ken Miller's refutation of Michael Behe's design argument. But these objections can't both be true. If ID can't be falsified, then scientific evidence can't falsify it. And if evidence can falsify it, then ID can't be unfalsifiable. Such contradictory objections should arouse our suspicions. Being open to evidence from nature is perhaps the cardinal scientific virtue. This is why contemporary arguments for intelligent design spend a lot of time on empirical evidence, and only then defend design as the best explanation for the evidence. Unfortunately, critics of intelligent design have mostly avoided the actual arguments and evidence offered by design theorists.

At the time, I noted,

Actually, it's not so much that the critics avoid evidence as that - so far as I can determine - they do not acknowledge that evidence for design could exist. That is, if it is evidence, it cannot be evidence for design, and if it is evidence for design it cannot be evidence. Thus, no matter what Gonzalez found about the unusually favourable position of Earth in the galaxy, that could not - by definition - be evidence for design. And anyone who suggests it might be could lose their job or fail to get tenure as a prof. To the extent that the anti-ID folk see science as the accumulation of evidence that things were not designed, there is no chance of the two groups discussing evidence in a fruitful way.

And of course, the recent revelations from the e-mail trail showed how far they were from even considering discussing the evidence.