Tuesday, September 29, 2009

Off Topic: Dark Matter Hunter

Wired has a story on attempts by physicists to find the elusive Dark Matter that "must" be there. The story, by Brandon Keim notes:
“Even if we don’t know what dark matter is, we know how it must act,” said Eduardo Abancens, a physicist at Spain’s University of Zaragoza and designer of a prototype dark matter detector.

According to physicists, only around five percent of what makes up the universe can presently be detected. The existence of dark matter is inferred from the behavior of faraway galaxies, which move in ways that can only be explained by a gravitational pull caused by more mass than can be seen. They estimate dark matter represents around 20 percent of the universe, with the other 75 percent made up of dark energy, a repulsive force that is causing the universe to expand at an ever-quickening pace.

At the heart of Abancens’ team’s detector, which is called a scintillating bolometer and resembles a prop from The Golden Compass, is a crystal so pure it can conduct the energy ostensibly generated when a particle of dark matter strikes the nucleus of one of its atoms.

Three things struck me about this story. First, it is really cool that modern technology can come to the aid of physicists in this way. Two, this is how science is supposed to work, with hypothetical questions being answered in either confirmation or non-confirmation of a theory (existence of dark matter). Three, if an evolutionist said anything like this, creationists would be sounding it from the rooftops and popping the champagne corks, celebrating the "death of evolution" as a theory. Every day, the Discovery Institute proclaims that evolution cannot explain this, that or the other. Funny how this never seems to apply to cosmology or astrophysics.

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Friday, September 25, 2009

Kevin Spacey in Inherit the Wind

Kevin Spacey is appearing in the play Inherit the Wind at the Old Vic, in London from September 18 through December 20. Charlie Piane of Broadwayworld.com writes:
Trevor Nunn says: "I directed scenes from this remarkable play when I was a student, and realized then just how electric and involving it could be for audiences. So I feel unusually fulfilled, more than a generation later, to be able to direct Kevin Spacey and David Troughton in this Titanic clash of ideas. The debate it presents, that goes to the heart of what freedom means in America, continues to find its way into the courtrooms of the United States in Darwin's Anniversary year. Somehow, I don't think Jerome Lawrence and Robert E.Lee would be surprised".
I would stop by if I could

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Birds to Dinosaurs: The Avalanche of Evidence Continues

PhysOrg is reporting on the discovery and description of a four-winged dinosaur that provides more evidence of the dinosaur-bird transition. The article notes:

Until now, A. huxleyi was thought to be a primitive bird. It was presumed to have been a near-contemporary of , the first recognised bird, which flew around 150 million years ago.

But these opinions were based on an incomplete fossil.

The new, nearly-complete specimen gives a different picture, suggesting that A. huxleyi is millions of years older than Archaeopteryx and has both dinosaur and avian features.

It is the long-sought evidence that proves birds descended from theropod dinosaurs, argues Xu.

Interestingly, when complete individuals of Archaeopteryx were discovered, several researchers went back to their drawers and pulled out what they thought were theropod dinosaurs and discovered that they had misclassified them! This find also continues to blow a hole in the creationism argument that focuses on Archaeopteryx being a bird and, thus, not descendant from dinosaurs—an argument that grows more dishonest with every new discovery:

Scientists have long argued about the evolutionary line taken by birds.

Some have said bird-like dinosaurs appear too late in the to be the true ancestors of birds, an argument known as the "temporal paradox."

The debate has raged for years mainly because the fossil evidence is so rare or fragmented.

The new evidence comes from in Daxishan, in Jianchang county in northeastern China.

It was found in rock dated to the early part of the Late Jurassic, between 151 and 161 million years ago, which means it is clearly older than Archaeopteryx.

There is now a wealth of evidence for over two dozen different forms that show the transition from dinosaurs to birds. Time to stick this one in the "arguments that creationists shouldn't use" pile.

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When is Darwin Not Darwin?

Useless News and World Distort has an article on the giveaway of a particular version of Charles Darwin's On the Origin of Species by Means of Natural Selection. It has a rebuttal. Dan Gilgoff writes:

In time for the 150th anniversary of Charles Darwin's Origin of Species, a major Christian ministry is publishing an edition of the book that features an introduction rebutting the theory of evolution and making the case for intelligent design. The ministry, Ray Comfort's Living Waters, is distributing tens of thousands of free copies on college campuses nationwide.

Kirk Cameron, star of the '80s sitcom Growing Pains, has recorded a video promoting the project, above.

Lost on these people is that you can't make a scientific case for intelligent design. You can only make a case against evolution. Good luck with that one. From the Living Waters boilerplate:
This introduction gives the history of evolution, a timeline of Darwin's life, Hitler's undeniable connections to the theory, Darwin's racism, his disdain for women, and his thoughts on the existence of God. It lists the theory's many hoaxes, exposes the unscientific belief that nothing created everything, points to the incredible structure of DNA, and the absence of any species-to-species transitional forms. It presents a balanced view of Creationism with information on scientists who believed that God created the universe—scientists such as Albert Einstein, Isaac Newton, Nicholas Copernicus, Francis Bacon, Michael Faraday, Louis Pasteur and Johannes Kepler. It uses many original graphics and "is for use in schools, colleges, and prestigious learning institutions." The introduction also contains the entire contents of the popular booklet, "Why Christianity?"
Not dead sure what any of that has to do with evolution, since none of the people mentioned is a biologist. And what is Kirk Cameron's profession? Oh yeah, he's an ACTOR. He is not a biologist. He has no biological training. The arguments are old, tired and have been rebutted so many times that there is simply no excuse for them. No wonder the scientists are hopping mad. Flat-earth christianity marches on.

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Thursday, September 24, 2009

Darwin and Faith

Nick Spencer of the Guardian has an interesting article on Charles Darwin, evolution, and faith. Titled Darwin's Complex Loss of Faith, Spencer argues that Darwin's work on evolution did not kill his faith in God, but did alter it dramatically. Spencer also puts this in historical context:
Up until his return from the Beagle in 1836, Darwin considered himself an "orthodox" Christian. There is no reason to doubt this although it is important to recognise that his orthodoxy was a specific early 19th century, rational, demonstrable, civilised, gentlemanly kind of orthodoxy. In particular, it was heavily influenced by William Paley whose Natural Theology confidently argued that nature contains "every manifestation of design… [that] design must have had a designer … That designer must have been a person [and] that person is God." Christianity for Darwin was primarily a proof to be established and Paley did that admirably.

When his emerging theory began to undermine these ideas, it also undermined the Christianity that was built on them. It didn't happen immediately. Darwin's notebooks show him trying to accommodate an intellectually credible idea of God and his new theory – in many ways successfully.
It had only been recently that new ideas of the age of the earth and coldly factual observations of the geological record had radically revised science's understanding of the earth and its inhabitants. Darwin's faith was not unusual in that respect. As Spencer correctly points out, it was not evolution that separated Darwin from God:

When, however, his daughter Annie died in 1851, aged 10, suffering moved from being a theoretical problem to an agonisingly personal one. Most Victorian families lost children (Darwin himself lost two others in infancy) but Annie was his favourite and, unlike most Victorian fathers, he had witnessed every last, degrading moment of her short life. The experience destroyed what was left of his Christian faith.

The claim that evolution destroyed Darwin's faith is, thus, only a half-truth, usually made to prove somehow that evolution killed God. By the same reckoning, the claim that evolution had nothing to do with his loss of faith (which was entirely due to Annie's death) is no more accurate, and is often made for equally polemical purposes (usually to demonstrate that evolution presents no challenges whatsoever to religious belief).

I would posit that a faith that sees evolution as a threat to the very existence of God is not a very strong faith and certainly one that is worth examining.
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Wednesday, September 23, 2009

William Dembski and Jello

In the gufuffle about the new Dembski/Marks paper that, according to them and the Discovery Institute, constitutes evidence against evolution, several people across the blogosphere have commented on the paper by David Wolpert from 1997 that took Dembski's application of the NFL theorems to the woodshed. It is every bit as devastating as the testimony by Jeffrey Shallit for the Dover-Kitzmiller trial. This is even more true because Wolpert is the co-creator of the No Free Lunch theorems, along with William Macready1. Wolpert's article is titled William Dembski's treatment of the No Free Lunch theorems is written in jello, a title that does not leave much to the imagination. So what are the No Free Lunch theorems? Wolpert writes:
These theorems, loosely speaking, say that the performance-weighted measure of domains in which some search algorithm A beats some contender algorithm B exactly equals the measure of domains for which the reverse is true. So, for example, in attempting to find a high point on a surface, a hill-ascending algorithm will perform no better than random search, and in fact no better than a hill-descending algorithm, over the space of all surfaces one might search. In short, according to these theorems there is no free lunch; without tailoring one's algorithm to the domain at hand, one has no assurances that that algorithm will perform well on that domain.
Dembski has taken the theorems and argued that if search algorithms are analogous to genetic changes in the environment and that genetic change is an "unguided random process," then no amount of evolutionary change will amount to anything. But Wolpert has concerns about how Dembski has applied the theorems and how well it applies to the biological world:
Indeed, throughout there is a marked elision of the formal details of the biological processes under consideration. Perhaps the most glaring example of this is that neo-Darwinian evolution of ecosystems does not involve a set of genomes all searching the same, fixed fitness function, the situation considered by the NFL theorems. Rather it is a co-evolutionary process. Roughly speaking, as each genome changes from one generation to the next, it modifies the surfaces that the other genomes are searching. And recent results indicate that NFL results do not hold in co-evolution.
The reason there is a marked elision of the biological details is that Dembski has demonstrated numerous times that he does not understand the biological details, having never worked in the field or studied how organisms change over time. As Wolpert and other people have pointed out, Dembski assumes the same fitness function for all environments. This in no way describes biological reality or how selection works. Why is it that Dembski refuses to acknowledge this?

1D. H. Wolpert and W. G. Macready, “No free lunch theorems for search,” Santa Fe Institute, Sante Fe, NM, Tech. Rep. SFI-TR-05-010, 1995.

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Tuesday, September 22, 2009

Saving the Distant Past

Palaeontologists at Mistaken Point, Newfoundland are working to preserve the distant past by making casts of the fossils. The fossils that are found on the Avalon Peninsula are estimated to be around 565 million years old. As CBC news writes:
"One advantage of casting is, obviously, is to show similar objects to a wider audience, which is the case here," said [Royal Ontario Museum] ROM associate curator of invertebrate paleontology, Jean-Bernard Caron.

"We are going to show the casts, not only in Newfoundland close to the site, but also at the Royal Ontario Museum, where a million visitors come through our doors every year."

The fossil casts will be shown in Portugal Cove South, near Mistaken Point, about 135 kilometres south of St. John's, and at the Johnson Geo Centre, in St. John's.

People have damaged some of the fossils on the site by walking on them. Other fossils have been chiselled out of the rock.
Hats off to the ROM!

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Monday, September 21, 2009

Evolution of the Four-Chambered Heart

Creationism lost another icon today when it was announced by the Gladstone Institute for Cardiovascular Disease that a gene in the four-chambered heart can be traced to turtles and other reptiles. E-Science News writes:

"This is the first genetic link to the evolution of two, rather than one, pumping chamber in the heart, which is a key event in the evolution of becoming warm-blooded," said Gladstone investigator Benoit Bruneau, PhD, who led the study. "The gene involved, Tbx5, is also implicated in human congenital heart disease, so our results also bring insight into human disease."

From an evolutionary standpoint, the reptiles occupy a critical point in heart evolution.

It has always been a tenet of creationism that the four-chambered human heart could never have evolved by itself and that this constitutes evidence against evolution. The writer continues:
During evolution, new genetic regulatory elements evolved to tell the Tbx5 gene to form a sharp boundary of Tbx5 expression. This resulted in two ventricles. Researchers will now work to identify those genetic regulatory mechanisms during the evolution of reptiles. The work also has important implications for the understanding of congenital heart defects, which are the most common human birth defect, occurring in one out of every one hundred births worldwide. Humans born with only one pumping chamber, resembling frog hearts, suffer the highest mortality and require extensive surgery as newborns.
As Kenneth Miller says: "Never bet against science."

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Richard and Judy Wonder Why

The Daily Express has an editorial by "The Nation's Favourite TV Couple," Richard and Judy on the rejection of evolution in the United States. The first line, describing the rejection of evolution by nearly 60% of the American public nearly made me snort a sandwich through my nose:
SOMETIMES a statistic leaps off the page, grabs one by the ears and shakes hard.
Yes, it does. The column is mostly lighthearted disbelief but along the way, there is a very, very, very sobering observation:
The same people who mock fundamentalist Islamists for believing that suicide bombers are martyrs, to be rewarded in paradise with honey and patiently-queueing virgins, will confidently tell you that God created the world in six days (ie 144 hours) and that all living things – dinosaurs, hummingbirds, elephants, sabre-toothed tigers, cockroaches and human beings – appeared in the same instant.

Sad, but true.
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Sunday, September 20, 2009

"The Cooking Ape"

The Times Online has a story on human evolution and cooking that will, likely, not sit well with some people:
It is the ultimate domestic cliché: a woman, pinafored and dutiful, tending a stove all day in preparation for her husband’s homecoming. As soon as he walks in, the ritual can begin: family members take their seats around the table (he sits at the head, of course) and dinner is served. Our couple are reliving a scene that has played out billions of times in our history because gender roles — husband at work all day, woman as homebody — have been forged not by relatively recent social conventions but by our distant evolutionary past.
Come again? The current notion of primate evolution is that the social groups are largely mirrored by current ape configurations. The prime mover behind this idea is Richard Wrangham, who argues that the world revolves around food:
Early human marriages, he suggests, were “primitive protection rackets”, in which men protected women from hungry marauders (attracted by the smoke of the fire) in return for a hot meal at the end of the day and, almost as an afterthought, babies. This is a radical notion — that domestic unions are mainly about food, not sex — but it’s not ridiculous. Anthropologists have noted that many primitive societies will tolerate a married woman sleeping around, but will ostracise her if she feeds any man other than her husband. In the ancestral struggle for survival, it seems, sustenance was more important than sex.
It is well known that the drive to eat trumps the drive for sex (but not by much). The anthropologist J. Lawrence Angel once said that "when two groups of people meet, they may fight, but they will always mate." I will be curious to see how well this is received.

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Orchids, Evolution and a "Creation Confirmation"

My son Marcus goes to a private Christian school that, while having a great curriculum in history, languages, grammar, mathematics and Bible, uses creationism as its basis for science. To that end, each year they learn about a different topic from a slightly peculiar point of view. This year it is botany. We tootle along in the book, explaining monocots, dicots, carnivorous plants and so on. Interspersed among these safe topics are these "Creation Confirmation" sections. The book is from Apologia Education Ministries and is written by Jeannie K. Fulbright. Apologia's page has this to say about her:
Following graduation and marriage, her writing and speaking focused on building up the Christian community, teaching marriage and parenting classes, in addition to writing articles and Bible studies. After her homeschool journey began, Jeannie discerned an immense need for Creation-based, scientifically sound, engaging, easy-to-use science curricula.
In other words, she doesn't have any education in palaeontology or biology. Is this what they mean by "scientifically sound?" One of these passages focuses on orchids, long a controversial issue among palaeobotanists, only in the sense that it is not clear when they evolved. She writes:
Orchids give us further evidence against evolution. Flowers don't use nectar for themselves. They only use it to attract animals to help them in pollination. Flowers spend a lot of energy making nectar that just gets eaten by the animals. Since orchids like the bee orchid get pollination without actually feeding the animals, survival is easier for them. They don't have to keep making food for animals. Evolution would say that since these orchids have an easier time surviving than orchids that actually feed animals, they should be the main kind of orchids in creation. Why, then are they rare compared to other orchids? Only a few orchids attract animals by imitation. Most of them use a lot of energy making food for animals in order to attrack them. The fact that most orchids (and flowers in general) produce nectar for animals to eat shows that God intended flowers and animals to work together to survive. 1
Where to start. She manages to write about orchids without ever mentioning the pollinarium, a key feature of these plants. As Johnson and Edwards (1999) write:
The packaging of pollen into a compact unit known as the pollinium, which together with accessory structures for attachment to pollinators comprises a pollinarium, was undoubtedly a key innovation in the evolutionary history of the Orchidaceae, and may have played a role in promoting the tremendous radiation of the group, which numbers at least 19 500 species (Dressier 1993).2
But, of course, this doesn't explain why the Bee Orchid is less prolific than other orchids. Why would this be the case? Subsequent to the publishing of On the Origin of Species by Means of Natural Selection, Darwin wrote about, you guessed it, orchids. In the work of Darwin on the Orchid family is an explanation for why this is. As Johnson and Edwards put it:
The majority of orchid species (and most flowering plants) are hermaphroditic: each individual possesses both male and female reproductive organs. Hermaphrodism might seem like a good way of ensuring reproductive success and hence evolutionary persistence. But Darwin was convinced that self-crossing—and even mating between relatives—decreased the survival and reproductive abilities (the "vigor and fertility") of the offspring produced (e.g., 1859, 96-97; Darwin worried about how bad it might have been for his own children that he had married his first cousin, Emma; see Desmond and Moore 1991, 575). The more hermaphroditic plants he studied, the more mechanisms he found for the promotion of intercrossing. Among orchids, self-crossing was exceedingly rare. Darwin knew of only one case, the bee orchid, Ophrys apifera (which he predicted would go extinct, and he confided that he wished he could live a thousand years in order to see the last one go; see Desmond and Moore 1991, 511-512).3
Myriad examples exist in nature of the means of increasing genetic variability in any given offspring generation. Even among humans, not only is there a mixing of the genetic traits of the mother and father, but there is crossing over of homologous chromosomes to further increase genetic variation. Darwin's lament is the lament that is echoed by most societies in the world, who have taboos against inbreeding. Inbreeding does two things: it restricts the amount of potential genetic variation in the next generation and it also results in the expression of recessive deleterious traits that might otherwise be hidden in the next generation.

The point behind the above is that this is classic Mendelian inheritance, something that is taught in high school biology classes. It took me very little time to run down the reason for the comparative lack of heartiness of the Bee Orchid, something Ms. Fulbright couldn't be bothered to do. Consequently, the question she asks is very easily answered within an evolutionary framework and constitutes no evidence against evolution whatsoever.

1Fulbright, Jeannie K. (2004) Exploring Creation with Botany. Anderson, Indiana: Apologia Education Ministries, Inc. p.54

2Johnson, S.D. and Edwards, T.J. (2000) The structure and function of orchid pollinaria. Plant Systematics and Evolution 222: 243

3Beatty, John (2006) Chance variation: Charles Darwin on Orchids. Philosophy of Science. 73: 629-641.
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Saturday, September 19, 2009

More Trouble For Dembski/Marks Article

P.Z. Myers at Pharyngula takes on the new article by William Dembski and Robert Marks. He pretty much takes off where we last left off:
Unbelievable. Dembski is bragging about getting a peer-reviewed paper published — in IEEE Transactions, so not a biology journal, and it's a paper about search algorithms — and he misrepresents Dawkins again. He just had to toss in his garbled version of the "Methinks it is a weasel" program in which Dembski has consistently gotten the algorithm stupidly wrong, and he does it again. The man really doesn't understand selection at all.
No, he doesn't. He has pretty much demonstrated that time and time again. Probably the most telling aspect of the whole affair, and one that shows again that Dembski does not behave like a real scientist is how he reacts. Here is what Myers says:

To make it even more amusing and even more like a standard creationist on the web, people pointed out to him in the comments that he was still getting it wrong, and what does he say?

I'm growing weary of these quibblings and thus shutting the comments off.

Of course, Bill, of course. We expect you to stick your fingers in your ears and shout "LALALALALA" all the time. Why not just get rid of the troublesome comments at your site altogether?

This is not the first time that Dembski has done this. For the Dover-Kitzmiller trial, Jeffrey Shallit offered expert testimony on why William Dembski is not a credible witness. This is what he writes about Dembski's unwillingness to respond to critics:
One of the characteristics of pseudoscientists is their unwillingness to forthrightly address critics of their work. In this characteristic (and others), Dembski places himsel firmly in the camp of pseudoscientists. David Wolpert, for example, the co-discoverer of the "No Free Lunch" theorems that are the major theme of Dembski's 2002 book, criticized Dembski's work in a review in Mathematical Reviews. Wolpert wrote that Dembski's arguments are fatally informal and imprecise". Dembski has not responded to Wolpert.

Mark Perkah addressed many of Dembski's arguments in his work, Unintelligent Design, but Dembski has never responded. I have criticized many of Dembski's argument in my review in BioSystems, pointing out, among other things, that the centerpiece calculation of No Free Lunch is off by about 65 orders of magnitude. An error this large in a legitimate scientific or mathematical publication would normally merit an immediate public correction, but Dembski has never acknowledged this error or my other criticisms.
This is not so different from the folks at the Discovery Institute not publishing their email addresses. A paper like this should draw all kinds of responses. Invariably, some of them will not be positive. If Dembski were a real scientist, he would welcome these comments and learn from them, instead of shutting them off and putting forth the same, old arguments that have been rebutted time and time again and that the scientific world quit taking seriously years ago. As one of the readers commented on Secular Cafe,
"This coming so shortly after his assigning his students the task of defending ID at hostile websites, I found it funny that he couldn't defend his own paper on his own website."

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Friday, September 18, 2009

Dawkins: Creationism Mostly a US Problem

The Irish Times has a short story on Richard Dawkins. Dawkins gave a speech in Dublin, at the RDS Concert Hall. Genevieve Carbery writes:

Dawkins said that while creationism was still largely an American problem, we needed to take stock of what was going on in the United States.

On this side of the Atlantic, Dawkins said that an influx of a very large Muslim population was difficult for scientists because Muslims believe that every single word of the Koran is true.

It may very well be that Islamic creationism will prove to be a more potent enemy than Christian fundamentalist creationism.

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Mini Precursor to Tyrannosaurus rex.

The Washington Post (and other organizations) is reporting on a surprising find linking the ground-shaking Tyrannosaurus rex to a precursor that was maybe nine feet high, on a good day. The find, though, is problematic in non-palaeontological ways:
The new animal, based on a single fossil smuggled out of China and eventually sold to a private collector, has been named raptorex. It lived 125 million years ago in a lake-dotted region of northern China.

Raptorex had a big head, tiny forelimbs, and a body built for sprinting, just like T. rex. But this fossil is of a young adult dinosaur, nearly full-grown, that at maturity would have been only about 9 feet long, compared with about 40 feet for an adult T. rex, according to a paper published Thursday in the online edition of the journal Science. It would have weighed only 150 pounds. An adult T. rex could reach 13,000 pounds.
That it has seen the light of day is great. That we have no idea what its provenance is is not. More good sites have been ruined by careless dinosaur hunters than I can care to count. The jarring morphology of Raptorex is confusing though:
"No longer can we describe the big head, the powerful jaw muscles, the tiny forelimbs, the very fleet-footed hind limb, as features of the very large body size and the mega-predatory habits," said study co-author Steve Brusatte, a doctoral candidate at the American Museum of Natural History in New York.
It should be pointed out that this poses no problems for evolution or dinosaur research. It simply means that evolution proceeded on a slightly different course for Tyrannosaurus than we thought. It is still clear that the morphology found in Raptorex was carried over into descendant forms.

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New Peer-Reviewed Article Said to Support Intelligent Design

William Dembski and Robert J. Marks have written an article titled: Conservation of Information in Search: Measuring the Cost of Success, which appears in IEEE Transactions on Systems, Man, and Cybernetics—Part A: Systems and Humans. The Discovery Institute has trumpeted (by none other than Casey Luskin) this article as being a "New Peer-Reviewed Scientific Article From William Dembski and Robert Marks Challenges the Creative Mechanism of Darwinian Evolution." As an aside, I am not sure how he has managed to snag a free, postable copy of this article, because we pay through the nose for our IEEE access. IEEE may have done this because Dembski is a senior member of the IEEE and, of course, a Discovery Institute fellow. Luskin writes:
Darwinian evolution is, at its heart, a search algorithm that uses a trial and error process of random mutation and unguided natural selection to find genotypes (i.e. DNA sequences) that lead to phenotypes (i.e. biomolecules and body plans) that have high fitness (i.e. foster survival and reproduction). Dembski and Marks' article explains that unless you start off with some information indicating where peaks in a fitness landscape may lie, any search — including a Darwinian one — is on average no better than a random search.
Note that Luskin uses the "unguided natural selection" language that he so heavily castigated Kenneth Miller for using. Beyond that, though, this is a peculiar read of how evolutionary theory works. Is this how a search algorithm really proceeds? It certainly is not how evolution proceeds. Luskin writes that:
This paper is in many ways a validation of some of Dembski's core ideas in his 2001 book No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence , which argued that some intelligent input is required to produce novel complex and specified information.
When it was released, No Free Lunch was criticized not so much as being wrong as being irrelevant to biological organisms. Dembski and Marks write:
The no free lunch theorem (NFLT) likewise establishes the need for specific information about the search target to improve the chances of a successful search. “[U]nless you can make prior assumptions about the . . . [problems] you are working on, then no search strategy, no matter how sophisticated, can be expected to perform better than any other”
In this example, he is equating (if I understand it correctly) each genetic variation with a term in a search algorithm. Basically, he is stating that genetic variation, left to its own devices, won't turn up anything complex no matter how many iterations it goes through. In this instance, all fitness functions are averaged. Here's the problem: in no environment are fitness functions averaged. That is like saying that the earth has one climate all over and that it imposes no selection pressures. Mark Chu-Carroll of Good Math, Bad Math also makes this observation:
Search algorithms work because they're not intended to succeed in all possible landscapes - they're designed to work in specific kinds of landscapes. A successful search algorithm is designed to operate in a landscape with a particular kind of structure. The performance of a particular search is tied to how well suited the search algorithm is to the landscape it's searching. A hill-climbing search-algorithm will work well in a continuous landscape with well-defined hills. A partitioning landscape will work well in a landscape that can be evenly partitioned in a well-defined way.
Dembski has, in the past, as in this example, used the Dawkins model of selection in which Dawkins runs through a series of non-random iterations (how evolution would actually proceed) in which a meaningless string slowly becomes METHINKSITISAWEASEL. This model of evolution is echoed by H. Allen Orr, who writes:
First consider the odds of forming this target sequence by blind chance, i.e., with monkeys at word-processors. Draw a random letter from the alphabet for the first position in the phrase; now another for the second position, and so on. The odds that you've spelled out the phrase METHINKS… are essentially nil: in fact, with twenty-six letters plus a blank space, the odds of getting the word METHINKS alone are already less than one in 280 billion. But now consider the following "evolutionary algorithm." Start with a random sequence as before but i) randomly change each character that doesn't match the target sequence; ii) if a resulting character matches the target keep it and in the next round change only those characters that don't match. So, if we start with SATHINKS, at the next step we'll randomly change only the first two letters; and if those changes yield MQTHINKS, then at the next step we'll randomly change only the second letter. This two-step evolutionary algorithm of mutation plus selection arrives at the phrase METHINKS… with surprising speed.
Dembski and Marks argue that there is specified information in this algorithm in that you know the outcome. Without this eventuality, they argue, an evolutionary algorithm will never amount to any new information. As Dawkins has correctly pointed out, though, the METHINKSITISAWEASEL algorithm is not strictly correct—it has a known endpoint—while evolution, as we understand it, does not (a knowable one anyway). Dawkins is trying to illustrate the concept of selection. That he does so in a seemingly teleological fashion does not detract from what the example is trying to illustrate. Further, as Chu-Carroll notes, Dawkins' METHINKS is not a simple lock-in-place example, as Dembski and Marks contend. They intentionally ignores the selection aspect of the illustration to focus on the idea that Dawkins has introduced exogenous/active information (the endpoint is known). Indeed, as Mark Perakh has written:
Evolutionary algorithms may be both targeted and targetless. Biological evolution, however, has no long-term target. Evolution is not directed toward any specific organism. The evolution of a species may continue indefinitely as long as the environment exerts selection pressure on that species. If a population does not show long-term change, it is not because that population has reached a target but because the environment, which coevolves with the species, acquires properties that eliminate its evolutionary pressure on the species. Dawkins’s weasel algorithm, on the other hand, stops when the target phrase has been reached.
For Dembski and Marks, it is an either or proposition. For a search algorithm to be successful, it must have active information. This, as the authors see it, contradicts the "random" nature of evolution. If there is no active information, then the search is no better than random and evolution reaches a dead end. Dembski and Marks conclude:
If any search algorithm is to perform better than random search, active information must be resident. If the active information is inaccurate (negative), the search can perform worse than random. Computers, despite their speed in performing queries, are thus, in the absence of active information, inadequate for resolving even moderately sized search problems. Accordingly, attempts to characterize evolutionary algorithms as creators of novel information are inappropriate.

The problem, as I see it, is that, while Dembski and Marks understand how these theorems work, they have no understanding of how evolution proceeds in the wild. They consistently say that some things cannot happen, when biologists have been observing them for hundreds of years. So, is this an article that supports ID while showing that evolution cannot happen? No, it isn't. Once again Dembski and Marks have applied inappropriate mathematics in attempting to show that evolution doesn't work. The argument fails because neither Dembski or Marks understand how evolution actually works. If the Discovery Institute continues to trumpet the fact that they have a peer-reviewed article that challenges evolution, when in fact, it does no such thing, such posturing will be dishonest.

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New Rules For Contesting "Traditional Theories" in Louisiana

Will Sentell of the Louisiana Advocate has a story on new rules that parents can use to excuse their children from certain objectionable school subjects. He writes:

The state’s top school board Wednesday approved procedures for residents who object to materials that challenge the teaching of evolution in public school science classes.

The rules, which were praised by evolution critics, stem from a law approved last year by the Legislature.

Backers say the law is needed to give science teachers more freedom to challenge traditional theories, including Charles Darwin’s theory of evolution.

What other traditional theories are they going to challenge? What about gravity? After all, no one has ever seen a black hole. What about germ theory? What about quantum mechanics? Nobody has ever seen a meson or a lepton or a quark. And searching for the Higgs Boson? forget it. Conceivably, if you believed that the earth was created six thousand years ago, you could complain about astronomy, biology, geology and physics. The only things open to you would be history and grammar. He continues:

The five-member panel will determine whether the materials:

  • Promote any religious doctrine, which is banned by the state law.
  • Are scientifically sound.
  • Are appropriate for the grade.
I would have more faith in this procedure if I had more faith in your local school board to be minimally educated in the sciences.

Thursday, September 17, 2009

Creationism in South Florida Politics

TampaOnline has a story about St. Petersburg mayoral candidate Bill Foster and whether his creationism will become a factor in the race. Some think that it is relevant:
"This city is trying to increase its employment base with respect to scientific organizations and trying to recruit scientific concerns to come here,'' said St. Petersburg architect Michael Dailey, who supports Kathleen Ford, Foster's opponent. "If our mayor has a belief system that basically rejects science, how can people take him seriously?"

So what exactly does he believe?

Foster, a member of Starkey Road Baptist Church in Seminole, dismissed the suggestion that each of those "days" could represent a period of thousands of years.

"In the Genesis account, it's timed by the sun and the moon,'' he responded.

Normally, candidates in the Tampa Bay area are not asked about dinosaurs or whether they believe the world is billions of years old or thousands, as some creationists maintain. (Ford said billions, Foster declined to answer.)

But in this election Foster has been dogged by questions about his religious beliefs after he sent a controversial letter to the Pinellas School Board, urging members to allow discussion about alternatives to the theory of evolution, such as the Genesis account. His letter suggested that Darwin contributed to the rise of Hitler and the Columbine massacre.

Another person for which science education has utterly failed.

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Video on Transitional Fossils

A video on Tangle, a community for Christians, by Agent Orange goes through the evidence for transitional fossils, with musical accompaniment. There is no way to embed it so here is the link.
http://www.tangle.com/view_video?viewkey=30f3c826e7d8c017176a. There are a number of other videos there. The quality is iffy but the presentation is good.

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More on the ERV - Human Interaction

The Irish Times has a story on how Endogenous Retroviruses have become part of the human genome. They write:

If you think that viruses have played no part in human evolution think again. Up to 46 per cent of our DNA was actually provided some time in the past by invading viruses, Ryan says. In comparison, just 1.5 per cent of our genomes arise from the genes we inherit from our primate and animal ancestors.

Ryan argues that Human Endogenous Retroviruses, or Hervs, are a viral integration process integral to the genome of all mammals. It came about by an extensive series of retroviral epidemics that infected our ancestors over tens of millions of years. This means that the virus is something more than just a pest.

ERVs have been used extensively as evidence for evolution, since we share a large number of ERVs with the higher primates and the insertion points are always the same. But as evil as they are, they also play continuous roles in our genome:
Ryan suggests that certain viruses play vital roles in human activity. “There are eight full-length viruses in the human placenta playing different roles, such as a human virus that codes for syncytin 1, which fuses cells together to create a protective layer between mother and baby,” says Ryan. “Proof of the symbiotic inclusion of such viruses as part of our DNA is the fact they have been conserved throughout evolution.”
ID has difficulty explaining ERVs because they cause such harm to any given generation and they are clearly detrimental to health in the short term. Here is a reminder of how important ERVs are to evolutionary studies.

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Wednesday, September 16, 2009

The New Humanist Takes on Adnan Oktar

Creationist extraordinaire Adnan Oktar (neé Harun Yahya) has a profile in the New Humanist. It is not pretty. The piece, entitled Sex, Flies and Videotape, by Halil Arda, follows the rise of the young Oktar through the ranks of Turkish society. Along the way, some truly scary things emerge:
While Oktar was building a public profile through his books, the real work was taking place backstage, as he began to assemble a group of followers dedicated to his twisted vision. Combining his undoubted charisma (something even his most ardent opponents concede) with a gift for manipulation, Oktar set out to build a cult around himself, drawing extensively on the techniques pioneered by messianic gurus like Charles Manson and Jim Jones, and in particular employing the strategies of the Moonies, the Bhagwan Shree Rajneesh and Scientology in targeting disaffected but affluent and educated young people, insisting they turn their worldly goods over to the cult, and vigorously enforcing rigid hierarchies and punitive rules.
Creationism and Islamic fundamentalism—what a combination. We also learn something about the scholarship of the man, himself:
It is highly doubtful whether any of these books – or indeed any of the 150 books he claims to have written – were actually written by Oktar. Berk, who was part of the inner circle at the time, confirms this: “There is a group of followers who are commissioned to write the books. For every book, they will take a few key sources written by Christian creationist authors, mostly from the US. They plagiarise the chapters and paragraphs that agree with their creationist approach. Then they add the photos, a few ayat from the Koran, and sometimes a bit of a commentary. None of the ideas belong to Oktar.”
As much as anything, it is his connexions to creationism in the United States that are troubling. In the past the Discovery Institute has accepted the outstretched arm of Oktar, in the mistaken belief that what they don't have in common is unimportant. Read the whole thing.

Another Exoplanet

Too bad its too hot. USA Heute is reporting on a planet that circles its parent star every 20 hours—that's kind of fast, I think—but is so hot it can't sustain life. The difference is that it is a rocky planet:
This is a major discovery in the field of trying to find life elsewhere in the universe, said outside expert Alan Boss of the Carnegie Institution. It was the buzz of a conference on finding an Earth-like planet outside our solar system, held in Barcelona, Spain, where the discovery was presented Wednesday morning. The find is also being published in the journal Astronomy and Astrophysics.

The planet is called Corot-7b. It was first discovered earlier this year. European scientists then watched it dozens of times to measure its density to prove that it is rocky like Earth. It's in our general neighborhood, circling a star in the winter sky about 500 light-years away. Each light-year is about 6 trillion miles.

Four planets in our solar system are rocky: Mercury, Venus, Earth and Mars.
Oh well. Next time.

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Tuesday, September 15, 2009

Creation Not Coming to the United States

This could only happen in the U.S. The film Creation, starring Paul Bettany and Jennifer Connelly has not been picked up by distributors in this country because of its subject matter. I was looking forward to seeing the film. Now, I might not get the chance! The article in the Telegraph hints at why this has happened:
Movieguide.org, an influential site which reviews films from a Christian perspective, described Darwin as the father of eugenics and denounced him as "a racist, a bigot and an 1800s naturalist whose legacy is mass murder". His "half-baked theory" directly influenced Adolf Hitler and led to "atrocities, crimes against humanity, cloning and genetic engineering", the site stated.
There is so much nonsense packed into that one paragraph that I doubt I will ever look at the site again. If their judgement and research is that bad about a film like this, I doubt it would be good about other films.

To say that the film makers were surprised is an understatement:

Jeremy Thomas, the Oscar-winning producer of Creation, said he was astonished that such attitudes exist 150 years after On The Origin of Species was published.

"That's what we're up against. In 2009. It's amazing," he said.

"The film has no distributor in America. It has got a deal everywhere else in the world but in the US, and it's because of what the film is about. People have been saying this is the best film they've seen all year, yet nobody in the US has picked it up.

And I doubt anyone will. What a shame.

UPDATE: John Scalzi doesn't think its the creationists that are keeping the film from coming to the U.S. He writes:
Alternately, and leaving aside any discussion of the actual quality of the film, it may be that a quiet story about the difficult relationship between an increasingly agnostic 19th Century British scientist and his increasingly devout wife, thrown into sharp relief by the death of their beloved 10-year-old daughter, performed by mid-list stars, is not exactly the sort of film that’s going to draw in a huge winter holiday crowd, regardless of whether that scientist happens to be Darwin or not, and that these facts are rather more pertinent, from a potential distributor’s point of view.
I don't buy it. Miramax thrives on such films and they have a huge market in this country. Currently in production or advertised are all kinds of film about dissolving relationships and general dysfunction. Furthermore, Lars von Trier's new film Anti-Christ, a movie about a husband and wife who lose a young son and try to get their lives back together, is getting extensive airplay, partly due to its extremely graphic sex scenes between the leads.

Along the way, Scalzi makes a somewhat cynical comment on the perceived sensibilities of the U.S. theatre-going public:
Maybe if Charles Darwin were played by Will Smith, was a gun-toting robot sent back from the future to learn how to love, and to kill the crap out of the alien baby eaters cleverly disguised as Galapagos tortoises, and then some way were contrived for Jennifer Connelly to expose her breasts to RoboDarwin two-thirds of the way through the film, and there were explosions and lasers and stunt men flying 150 feet into the air, then we might be talking wide-release from a modern major studio.
I still don't buy it.

Hat tip to Glenn Reynolds.

Monday, September 14, 2009

New Scientist Reviews The Greatest Show on Earth

Randy Olson of The New Scientist has a review of Richard Dawkins' latest book The Greatest Show on Earth. Olson is not so taken:
It's really kind of comical. If "spot the condescensions" is a new drinking game, then bottoms up! There's one in just about every chapter. Though Dawkins says from the outset, "This is not an anti-religious book", he can't help but knock religion throughout, For instance, he writes: "God, to repeat this point, which ought to be obvious, but isn't, never made a tiny wing in his eternal life." Young Earth creationists are, he writes, "deluded to the point of perversity". You get the sense that Dawkins just can't control it. It's as if he suffers from an anti-religious form of Tourette's syndrome.
This does not serve Dawkins in good stead. As he is seen increasingly as irrational about religion, the very people he is trying to convert increasingly ignore what he is saying because they are tired of being insulted. I know I am.

A New Kind of Geology Class

I think that if more people took a class like this, flood geology wouldn't be quite so well accepted. Clay Farris Naff of The Humanist (a magazine that I don't ordinarily read) has a good article on how geologist David Harwood, of the University of Nebraska at Lincoln, teaches his students to understand geology. Naff writes:
What would happen if the pro-science side quit trying to win over young people with words and instead let them discover science for themselves? That is what geologist David Harwood, holder of the Stout Chair in Stratigraphy at the University of Nebraska-Lincoln (UNL), decided to find out. Together with his former doctoral student, Richard Levy, he has created a unique geology field course for future teachers. The idea is simple: In the rocky wilderness of Wyoming, a dozen students are pressed into teams and tasked with recapitulating centuries’ worth of geological discovery in a matter of days.
It really isn't very simple. It took quite some time to understand the geology of the Rockies. Still, interesting things happen along the way. He writes about a particular student:

It soon becomes clear that everything he knows about science comes from the standard creationist cant. He brushes Harwood’s idea of science aside as “a lot of this’s and that’s. It all comes down to one word—theory.” It turns out that his main objection in this class is to the geological column, which sets the Earth’s age at billions of years. “It’s a hypothesis that can’t be proven or hasn’t been proven,” he says. “It’s not a fact.” To avoid the possibility of heresy, David avoids writing any dates at all in his field journal.

And yet, within a week, David’s mind opens up to new ways of thinking, and he becomes a vigorous advocate of the inquiry method of learning. That is not to say he drops his lifelong commitment to fundamentalist Christianity. That would be too much to expect. But change washes over him all the same like a baptism in broad-mindedness.

This is sad because it reminds me a bit of Glenn Morton's "conversion" from flood geology, which almost cost him his faith. If the church would simply teach good science to start with, then discoveries like this would not be so jarring for the average Christian who takes a class in geology. I wonder how many people who are "jarred" by information like this never find their way back to their faith.

Eagle From Hell

According to research coming out of Australia, a giant eagle may have been carnivorous after all. The story, in PhysOrg states:

Ken Ashwell of the University of New South Wales in Australia and Paul Scofield of the Canterbury Museum in New Zealand wrote their conclusions in the peer-reviewed Journal of Vertebrate Paleontology.

Using computed axial tomography, or CAT, the researchers scanned several skulls, a pelvis and a beak in an effort to reconstruct the size of the bird's brain, eyes, ears and spinal cord.

They compared their data on the Haast's eagle to characteristics of modern predator birds and scavenger birds to determine that the bird was a fearsome predator that ate the flightless moa birds and even humans.

Paul Scofield? Canterbury? What are the odds? Oh well, back to the story:
Scientists believe the Haast's eagle became extinct about 500 years ago, most likely due to habitat destruction and the extinction of its prey species at the hands of early Polynesian settlers. Before the humans colonized New Zealand about 750 years ago, the largest inhabitants were birds like the Haast's eagle and the moa.

Scofield said the findings are similar to what he found in Maori folk tales. "The science supports Maori mythology of the legendary pouakai or hokioi, a huge bird that could swoop down on people in the mountains and was capable of killing a small child," he said.
Although perhaps sensationalized, the story reminds one that the birds of the air are not the birds of yesteryear. The article doesn't say what the wingspan was but it must have been huge.

Friday, September 11, 2009

Ben Stein Being Sincere and Not So Sincere

Ben Stein, speechwriter for presidents, host of the great game show "Win Ben Stein's Money," which, sadly, is not still on, and narrator of the movie Expelled! has been fired from his gig writing for the New York Times. As if William Kristol's example wasn't enough of a warning to other conservative writers, the Grey Lady will simply broach no conservatism. I am convinced that David Brooks puts his job on the line every time he writes a column. There are also some unanswered questions about why Stein was fired and it is reasonable to conclude that the reasons that were given are not the truth, the whole truth and nothing but the truth. Along the way, however, he says some things that simply are not so. About the movie Expelled!, he writes the following:
Expelled was a plea for open discussion of the possibility that life might have started with an Intelligent Designer. This idea, that freedom of academic discussion on an issue as to which there is avid scientific disagreement has value, seems obvious to me. But it drives the atheists and neo-Darwinists crazy and they responded viciously.
No, it wasn't a plea for open discussion. Expelled! was a vicious diatribe against any and all things evolutionary, ending with the bald, unsupported claim that Darwin's views directly informed Hitler about how he was to treat people. This was complete with scenes of concentration camps, lest any viewer be unclear about just how evil evolution actually was. Furthermore, some of the cases that Mr. Stein profiled were not quite as he profiled them. See the excellent article "Expelled Exposed" for a recap of all of the claims and the holes in them. For added information about how dishonest the movie was, read this article by John Rennie and Steve Mirsky on "Six things in Expelled that Ben Stein doesn't want you to know." Does the end of destroying "Darwinism" really justify the means, especially when the means aren't very different from those that you decry?

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Mountain Building and Human Evolution

Did the uplift of mountains around the East African Rift Valley lead to the evolution of the earliest humans? Research by Royhan and Nahid Gani of the University of Utah, Energy and Geoscience Institute. As the article, in the University of Utah News Center notes:

They argue that the accelerated uplift of mountains and highlands stretching from Ethiopia to South Africa blocked much ocean moisture, converting lush tropical forests into an arid patchwork of woodlands and savannah grasslands that gradually favored human ancestors who came down from the trees and started walking on two feet - an energy-efficient way to search larger areas for food in an arid environment.

In their Geotimes article, the Ganis - a husband-and-wife research team who met in college in their native Bangladesh - describe this 3,700-mile-long stretch of highlands and mountains as "the Wall of Africa." It parallels the famed East African Rift valley, where many fossils of human ancestors were found.

"Because of the crustal movement or tectonism in East Africa, the landscape drastically changed over the last 7 million years," says Royhan Gani (pronounced rye-hawn Go-knee), a research assistant professor of civil and environmental engineering. "That landscape controlled climate on a local to regional scale. That climate change spurred human ancestors to evolve from apes."

We know that the earliest hominids begin showing up around five to six million years ago (Orrorin tugenensis, Ardipithecus ramidus and Australopithecus anamensis) and that this coincides with increased aridity and expansion of grasslands. This piece of information dovetails nicely into that theory.

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The Long Arm of the Discovery Institute

The topic of evolution and creationism seems to be a common thread in the Roanoke Times. Today, guest writer David Clark claims that "Evolution isn't even a good theory." Clark, according to the introduction, is on the staff of the Campus Bible Fellowship, at Virginia Tech. He writes:

The other major issue I see is the relationship between science and evolution. Some assume that evolution is science-based fact, but it is far from that. Evolution is a theory -- and not even a good scientific theory, because it is contrary to science. Evolution has never been observed. Micro-evolution has been observed, and from that scientists have theorized the possibility of macro-evolution by extrapolation, which is a huge stretch. Micro-evolution results in the loss of information while macro-evolution requires the creation of new information.

Evolution may have sounded reasonable in Darwin's day, but since the discoveries of the complexity of the simplest living cell and of DNA, plus the development of information science, amoeba-to-human gradual evolution is demonstrably false.

Sound familiar? This is the long arm of the Discovery Institute, pumping out misinformation faster than oil through a pipeline. Not a bit of the above is true. Mr. Clark first writes that evolution has never been observed. Then he writes that "micro-evolution" has been observed. Well, which is it? Since microevolution is evolution, clearly it has been observed. The idea that microevolution results in a loss of information only makes sense if you don't understand how evolution works (and it is not clear that anyone on the staff of the Discovery Institute does). In every generation, random mutations occur and then selection acts upon them depending on what sort of trait they confer and what the environmental impact on the trait is. Some are beneficial, quite a few are harmful, but the vast majority of them are selectively neutral. Consequently, they add to the genetic variability of any given population. Whether or not selection works on those traits in the future depends on how the environment or population changes.

He makes the claim that gradual evolution is demonstrably false. Aside from the fact that this is a bit of a straw man—evolution proceeds both quickly and slowly depending on the environment/selection interaction—I would like to know how he supports that claim, since the fossil record is filled with transitional forms at every major level. These include fossils that show the transition from land animals to whales, from dinosaurs to birds (lots of those: from Sinosauropteryx prima to Protarchaeopteryx to Archaeopteryx to Shenzhouraptor through a number of other forms to modern birds), from lobe-finned fish (crossopterygians) to early tetrapods (such as Icthyostega and Cassinaria). To be sure, it may very well be that there is no direct ancestor/descendent relationship in any of the above examples. That does not mean they are not transitional or that the trends were not heading in a particular direction. Dinosaurs exist in the late Jurassic and early Cretaceous that have feathers but were non-flying. They had feathers because feathers are marvelous insulators. Evidence exists for the evolution of five different kinds of feathers over time, culminating in the form we see in modern birds. Since evolution proceeds more like a bush than a tree, this is understandable. It is a mix of direct and collateral ancestry.

He closes with the following:
I'm in good company. Dr. Henry Morris, who was head of the Department of Civil Engineering at Virginia Tech from 1957 to 1970, authored more than 45 books on the Bible and creation. In 1970, he founded the Institute for Creation Research, which continues to promote six-day creation through literature and seminars. Some years ago, 25 professors at Tech signed a letter saying they did not accept evolution.
How is this good company? Henry Morris had no standing within the scientific community because he espoused ideas that were outside his areas of expertise and had been dismissed by scientists over a hundred years before he was born. Henry Morris, who along with John Whitcomb, wrote The Genesis Flood, believed that there had been a world-wide deluge that had created the fossil and geological record and had inundated the entire earth. As Christian geologist Davis Young put it in his History of the Collapse of "Flood Geology" and a Young Earth:

Just what are those extrabiblical data? In summary, several centuries of effort to locate physical remnants of the biblical deluge have completely failed. Any physical evidence that has been claimed to support a global flood has eventually been demonstrated to have a different explanation. The idea that the flood deposited the world's stratified rocks has been thoroughly discredited by numerous lines of evidence. Many of the individual strata give evidence of having been deposited in such non-flood environments as rivers, beaches, deltas, lakes, glaciers, deserts, and shallow oceanic platforms. Many strata, such as lake deposits and fossil reefs, contain abundant indicators of very slow deposition under environmentally sensitive conditions quite incompatible with a catastrophic deluge. Many strata are overlain by fossil soils and separated from higher strata by erosional breaks that could only have been produced over extensive lengths of time. The fossils themselves are arrayed in progressive order in the geologic column. Many of the organisms lived in environments utterly unlike flooded terrains. Radiometric dating of volcanic ash or lava flows interbedded with fossiliferous strata show that they are millions of years old. Some large masses of igneous rocks injected into the strata took hundreds of thousands of years to cool and crystallize. Many fossiliferous rocks have been metamorphosed, indicating extreme burial that could not possibly have occurred during a year-long deluge.

All the evidence of the rocks tells us that they were not produced or arranged by a flood. The views of earth history offered by Woodward, Catcott, G.M. Price, Whitcomb and Morris, and John R. Rice are simply and obviously incorrect.

I implore those like Mr. Clark to go out and read the actual geological and palaeontological literature. It is in these pages that evolution lives or dies as a theory, not in the pages of a book written by someone who has never examined the data. As Saint Augustine put it:
Often a non-Christian knows something about the earth, the heavens, and the other parts of the world, about the motions and orbits of the stars and even their sizes and distances,… and this knowledge he holds with certainty from reason and experience. It is thus offensive and disgraceful for an unbeliever to hear a Christian talk nonsense about such things, claiming that what he is saying is based in Scripture. We should do all that we can to avoid such an embarrassing situation, lest the unbeliever see only ignorance in the Christian and laugh to scorn.1
It was true when Augustine said it, it is true sixteen centuries later.

1 St. Augustine, De Genesi ad litteram libri duodecim (The Literal Meaning of Genesis)

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Thursday, September 10, 2009

Looking in the Wrong Place?

Research out of the University of Copenhagen suggests that we have been looking in the wrong place for a source of oxygen that had to have been present for life to evolve on earth at the end of the Proterozoic eon. The story, in ThaiIndian states:

By analysing the isotopes of chromium in iron-rich sediments formed in the ancient oceans, a scientific team, led by Professor Robert Frei at the University of Copenhagen in Denmark, has found that a rise in atmospheric oxygen levels 580 million years ago was closely followed by the evolution of animal life.

The data offers new insight into how animal life - and ultimately humans - first came to roam the planet.

“Because animals evolved in the sea, most previous research has focussed on oceanic oxygen levels,” explained Newcastle University’s Dr Simon Poulton, one of the authors of the research paper.

“Our research confirms for the first time that a rise in atmospheric oxygen was the driving force for oxygenation of the oceans 580 million years ago, and that this was the catalyst for the evolution of large complex animals,” he added.

Distinctive chromium isotope signals occur when continental rocks are altered and weathered as a result of oxygen levels rising in the atmosphere.

According to the research, oxygen levels began to rise around 2.8 Gya but dropped again and did not experience its second rise until around 580 Mya. This would put it after the the most recent (Kaigas) of the "snowball earth" periods (assuming that is a viable theory).

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There are new images from the revamped Hubble Telescope that are breath-taking. What a universe!

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Darwin's Dilemma

And as if on cue...I get a circular from the Discovery Institute advertising a new film called Darwin's Dilemma, which has this as part of its tag line:
This major documentary, the third in Illustra’s internationally-acclaimed intelligent design series, probes one of the great mysteries of science, the Cambrian explosion, when in a moment of geological time complex animals first appeared on earth fully formed, without evidence of any evolutionary ancestors.




As one of my readers commented on a similar post: "My default in the 'malice/ignorance' question with respect to creationists used to be ignorance. Over the last 10 years it has shifted to malice." It is difficult not to think that, given that they do not seem to care whether or not the information that they disseminate is correct, as long as it fits the narrative. As Donald Prothero writes:
The problem with the creationists' fascination with the Cambrian explosion is that its all wrong! The major groups of invertebrate fossils do not all appear suddenly at the base of the Cambrian but are spaced out over strata spanning 80 million years—hardly an instantaneous "explosion"! Some groups appear tens of millions of years earlier than others. And preceding the "Cambrian Explosion" was a long slow buildup to the first appearance of typical Cambrian shelled invertebrates."1
I can't wait to watch the film.

1Prothero, D. (2007) Evolution: What the Fossils Say and Why it Matters. Columbia University Press. p. 161

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Tuesday, September 08, 2009

Simon Barnes Goes on a Tear

Simon Barnes of the TimesOnline is peeved at both the fundamentalists and at Richard Dawkins. In a post titled Caw, is that black thing a bird or a pterodactyl? he laments that the use of science by both sides is causing more problems than solutions:

He [Dawkins] says that evolution is a fact. Fine. He also holds up the non-existence of God as a fact, but that can never be the case. If you believe in an ineffable God who started the whole business of evolution, that’s your business. It can’t be proved or disproved — and therefore, it’s beyond the scientist’s scope. You can’t prove you have a soul; you can’t disprove it either. You can believe that life continues after death, and all that anyone can say is good old you, I wish I did.

Dawkins is right to point out that biblical literalism is wrong. Religion has no more business interfering with fact than science has in messing about with belief. It is not religion’s place to tell us that God created light and then a couple of days later He created the Sun as an after-thought, and if you don’t believe that you will go to Hell.

And it is not the place of science to tell us that Christ did not die for our sins. Science deals in fact; religion deals with belief and faith. Throughout history, when science has revealed facts that contradict religious belief, belief has shifted its ground. These days, nothing remains but faith — but faith is unshakable, at least by science.


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The ESE Gains More Momentum

The Evangelical Statement on Evolution, which is being spear-headed by Steve Martin is gaining steam. He has put an update on his site: An Evangelical Dialogue on Evolution.

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New Pterosaur Print Discovered

A very large footprint of a pterosaur has been discovered in Korea. According to Discoveryon:
The footprint was discovered in geological stratum dating back 100 million years and is 35.4 centimeters in length and 17.3 centimeters wide.

There is a trace of three asymmetrical spurs, the typical appearance of a pterosaur.

Before the discovery, the largest pterosaur footprint was that of the Haenamichnus, which was found in the southwestern city of Haenam, South Jeolla Province.
For you Troy folks out there, that is more than a foot long by about half a foot wide. Neat.

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Friday, September 04, 2009

Modern Human Evolution

Daily Galaxy has an article on how human evolution has proceeded in the recent past and how it might continue into the future.

A team led by University of Wisconsin-Madison anthropologist John Hawks estimates that positive selection just in the past 5,000 years alone -dating back to the Stone Age - has occurred at a rate roughly 100 times higher than any other period of human evolution. Many of the new genetic adjustments are occurring around changes in the human diet brought on by the advent of agriculture, and resistance to epidemic diseases that became major killers after the growth of human civilizations.

"In evolutionary terms, cultures that grow slowly are at a disadvantage, but the massive growth of human populations has led to far more genetic mutations," says Hawks. "And every mutation that is advantageous to people has a chance of being selected and driven toward fixation. What we are catching is an exceptional time."

While the correlation between population size and natural selection is nothing new - it was a core premise of Charles Darwin, Hawks says - the ability to bring quantifiable evidence to the table is a new and exciting outgrowth of the Human Genome Project.

This is the convergence of population genetics, comparative anatomy and palaeontology to explain how humans have evolved. About natural selection, he writes:

Another recently discovered gene, CCR5, originated about 4,000 years ago and now exists in about 10 percent of the European population. It was discovered recently because it makes people resistant to HIV/AIDS. But its original value might have come from obstructing the pathway for smallpox.

"There are many things under selection that are making it harder for pathogens to kill us," Hawks says.

Population growth is making all of this change occur much faster, Hawks says, giving a tribute to Charles Darwin. When Darwin wrote in "Origin of the Species" about challenges in animal breeding, he always emphasized that herd size "is of the highest importance for success" because large populations have more genetic variation, Hawks says.

This is contrary to popular wisdom that shows that evolution proceeds faster in smaller populations because traits are expressed more often. Typically, larger populations slow evolution down because they are much closer to Hardy-Weinberg equlibrium. I also wonder about the statement that human evolution is proceeding faster now than at any time in the past. I do not think we have the resolution to determine that, even genetically. The human "bush" has gone through some remarkable changes even in the last 200 thousand years, with the successive appearance of archaic Homo sapiens and modern Homo sapiens, with regional characteristics present in many populations. It is doubtful that any of these changes would have happened had the population been as global as it now is.

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More Nonsense From the Discovery Institute

For some people and some organizations, it doesn't matter how often you correct their misunderstandings, they go right on believing in them. A new post from (lawyer) Casey Luskin on the Burgess Shale is just this kind of piece. He writes:
These fossils revealed a mystery: like other Cambrian fauna, these strange soft-bodied fossils appeared in the fossil record abruptly, without evolutionary precursors.

Darwin himself was aware of this problem in his own day, writing that the lack of fossil evidence for the evolution of Cambrian trilobites "must at present remain inexplicable; and may be truely urged as a valid argument against the views here entertained." Nearly 150 years after Darwin penned those words, biology textbooks are still observing things like, "Most of the animal phyla that are represented in the fossil record first appear, 'fully formed,' in the Cambrian." Indeed, the striking appearance of animals in the Cambrian explosion is captured in a recent article in Nature article commemorating the 100th anniversary of Wolcott's discovery, stating that "virtually all animal groups alive today were present in Cambrian seas."

How is this remotely a problem? What does Luskin think that Collins means when he says "groups?" In the previous sentence Collins refers to chordates as a group. That's some group! The phylum Chordata consists of all animals that have either a true vertebral column or a notochord. In the Cambrian you see the first few examples of chordates. Today, chordates number over 44 000 species and consist of cephalochords, urochords and vertebrates, none of which had diversified by this point. Within the vertebrates alone are Reptilia, Mammalia, the sub-class Aves (recall that Aves has been subsumed within Reptilia because of the shared ancestry of birds with dinosaurs, crocodiles and alligators) and a host of other classes. Absolutely none of the animals that make up the later fossil record show up in the Cambrian. Animals like bears and whales date to the last fifty million years.

The Cambrian "explosion" took place over the course of some 60-70 million years and included the appearance of the first hard-shelled organisms. Before the Cambrian, all the way back to the Archean, there is evidence of animal tracks. Luskin and other creationists continue to peddle this nonsense about how life in all of its grandeur simply appeared out of thin air in the Cambrian. I am no longer sure whether is it because they are ignorant or mendacious.

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