Monday, July 31, 2006

A Matter of Evidence

A post at the blogsite Telic Thoughts provoked a large number of comments. An exchange involving the author, Nick Matzke and Mike Gene is reproduced. A comment follows:

Matzke: The various problems with Behe's irreducible complexity argument are here.

Bradford: None of which addresses the central point of Behe's description. Empirical evidence for the evolution of multi-protein complexes is weak. It contrasts with the strong evidence for unicellular adaptation documented by point mutations and other single step events. The contrast is telling and not mitigated by homologous protein arguments.

Matzke: Funny, the evolutionists have used evolutionary models to make successful research predictions in top journals on one of Behe's favorite IC systems, the immune system. I guess we'll just have to chalk all that up to luck, eh?

And: Why do you think that the evolution of large protein complexes, involving many point mutations, should have been observed within the very few years that scientists have even been aware of these things? You might as well be asking for birds to evolve wings in the lab. It's a silly request. Science requires testable models and passed tests, not impossible requests for video-camera documentation of every event that occurred over billions of years.

Bradford: It was not a request. It simply notes the empirical discrepency in support for unicellular adaptation as opposed to the multi-protein complexes referred to. Your point about the historic nature of the proposed scenario only reinforces my point that evidence by extrapolation is unavoidable if you wish to contend, for example, that the enzymes that are component parts of universal metabolic pathways evolved in Darwinian fashion. Fashioning selection criteria (to) the evolution of metabolic pathway enzymes from precursor proteins and identifying what these precursors might have been would be a most entertaining post. Behe was much too indulgent in his choice of IC systems.

My response occurred prior to this next one by Mike Gene. Gene correctly puts his finger on a double standard in evidence. Note the contrast in Matzke's citation of practical barriers as reasonable explanations for limited empirical documentation and Gene's reference to the demands made of IDers by their critics.

Mike Gene: Now ain’t that interesting? Consider that many ID critics want a video-tape of the designer designing, along with a complete psychological profile of the designer, and independent evidence of his tools.

Saturday, July 29, 2006

Why ID Will Win in the End

Nancy Pearcey posted an excellent article detailing reasons why ID is destined to win out. Her italicized article follows. My comments are in standard print.

To hear some conservatives talk, there is no room for proponents of intelligent design (ID) in the "big tent." In recent months commentators such as John Derbyshire in National Review and George Will and Charles Krauthammer in the Washington Post have inveighed against ID. Warning that "the conservative coalition" is coming unglued, Will all but called on "the storm-tossed and rudderless Republican Party" to repudiate the ID movement.

Conservatives who hope to be on the winning side, however, may want to put their money on ID, even if they harbor a few reservations at present. Here's why. For starters, the affirmation of design is good for science. Like all knowledge, science is a pattern-seeking project. The human mind inherently seeks intelligible order. Thus the conviction that such an order exists to be found is a crucial assumption. No scientists are going to find their work diminished because they ground it in the search for an inbuilt design in nature.

Indeed, as sociologist Rodney Stark argues in To the Glory of God, modern science could have arisen only in a culture convinced that the universe is the creation of a rational mind--and is thus intelligible to our rational minds. This explains why science arose historically in medieval Europe, a period when western civilization was saturated with Christianity. Steve Fuller, a sociologist of science, offers this as one reason he testified for ID in the recent court case in Dover, Pa. "The idea that religion provided intellectual sustenance for science," he explained on a recent blog, is "obviously borne out by history."

By contrast, Darwinist theory claims that the design in nature is not real but only apparent, a product of blind, mechanical forces. As arch-Darwinian Richard Dawkins said in a recent Salon interview, evolution produces "the illusion of design." The implication for science, as Richard Rorty elaborates so clearly, is that truth is not "out there" to be discovered but is merely a social construction. Such postmodernist notions threaten to undercut the scientific enterprise.

The second reason ID will win is that, contrary to the way it is often portrayed, it does not thrive on "gaps" in science but rather on the growth of science. The argument from design first became popular during the scientific revolution, which revealed that nature is more intelligible than anyone had hitherto imagined. And the current resurgence of ID was spawned by the revolution in biochemistry, which revealed the complex engineering and information processing that goes on within the cell.

Indeed. The gap charge points to a Darwinian article of faith. It contends that data which cannot be incorporated into a Darwinian paradigm indicates a temporary state of affairs that eventually will be remedied with the advent of future knowledge. There is nothing wrong with believing that validation will occur. However if it is a scientific expression rather than an article of faith, proponents need to specify not only the type of test results that would validate theory but also results that would falsify it. The latter is conspicuously absent from exchanges evidencing the gap charge which Darwinists utilize as a rhetorical weapon.

We now know that the cell bristles with molecular machinery far more complicated than anything devised by mere humans. Each cell is akin to a miniature factory town, humming with power plants and automated factories, connected by criss-crossing transport rails and directed by a headquarters (the nucleus) housing a library of coded blueprints. The more we learn about life, the less plausible is any evolutionary theory that relies on blind, undirected, piece-by-piece change.

The molecular phenomenon has unmistakable parallels to familiar designed objects. But the belief that the above resulted from intelligent causality also rejects the alternative natural selection concept. Not only does natural selection, all too frequently, not suggest intermediate selection candidates, it is an empirically weak concept. Experiments do not document the evolution of the mentioned cellular constructs. Evidence offered is indirect and not supportive of evolutionary mechanisms to the exclusion of intelligence as a causal component.

Third, ID will win because it incorporates the insights of the high-tech world of information theory. The revolution in biochemistry revealed that the core of living things is a code, language, information (DNA). The origin of life has now been recast as the origin of complex biological information. This explains why laboratory experiments to create life have failed—because they work from the bottom up, by assembling the right materials. But life is not fundamentally about matter; it’s about information.

This is the strongest inference for intelligence. Encoded systems are the product of intelligent design. Another blog entry explores this in more detail.

In today's preferred analogy, the DNA molecule is the hardware, while the information stored and transmitted is the software. "Trying to make life by mixing chemicals in a test tube," writes astrophysicist Paul Davies, "is like soldering switches and wires in an attempt to produce Windows 98. It won't work because it addresses the problem at the wrong conceptual level.” The paramount role of information strongly suggests that mind preceded matter.

Eloquently stated and a repudiation of the contention that intelligence is an emergent property of matter.

Fourth, ID will win because it recovers the unity of truth. Edward Purcell in The Crisis of Democratic Theory: Scientific Naturalism and the Problem of Value explains how Darwinism led to a naturalistic worldview--one in which the natural sciences were elevated to the only form of objective knowledge while "theological dogmas and philosophical absolutes were at worst totally fraudulent and at best merely symbolic of deep human aspirations." In other words, Darwinism lent scientific support to the fact/value dichotomy, where religion and morality are dismissed as merely subjective and private, or even outright false.

As a result, ID appeals to a broad range of people concerned about overcoming the fact/value split--especially relevant during the Christmas season, when the ACLU and assorted secularists try to impose their gospel of privatized religion onto the rest of the country. As Richard John Neuhaus wrote recently in First Things, not just conservative Protestants but also "Catholics and everyone else have an enormous stake in defending the unity of truth." BBC's Washington correspondent Justin Webb recently asked why American social conservatives "are spending more energy fighting Charles Darwin than cutting taxes," but the reason is clear: At stake is not just a scientific theory but a divided concept of truth that reduces religion and morality to the level of myth.

As though to prove the point, at Kansas University the chairman of the religious studies department, Paul Mirecki, announced a new course subtitled "Intelligent Design, Creationisms, and other Religious Mythologies." Mirecki posted a note on a student atheists website bragging that he was "doing my part to [tick] off the religious right," giving them a "slap in their big fat face by teaching [ID] . . . under the category 'mythology.'" (Mirecki has since apologized.)

Which suggests the final reason ID will win--because it accords with the ideals of a free and open society. In our pluralistic age, schools should train students in critical thinking to prepare them to engage respectfully and intelligently with a wide range of worldviews, both religious and secular. Yet under current rules, public schools may present evidence for scientific theories that imply a strictly materialistic or secular worldview, while they are not allowed to present evidence for scientific theories that imply a non-materialistic or religious worldview (though the latter may be mocked and ridiculed, as the KU course proves).

The public cannot help but notice that many ID proponents are well educated and credentialed. Yet, as attorney Doug Kern writes in Tech Central Station, "the pro-Darwin crowd insists on the same phooey-to-the-booboisie shtick that was tiresome in Mencken's day." It has grown even more tiresome in our own day.

Darwinism's days are numbered.

Friday, July 28, 2006

A Nucleosome Code?

Remarkable news about a genetic code involved in the placement of nucleosomes has appeared in numerous sources recently. A biocompare news story entitled 'Scientists Discover A Genetic Code For Organizing DNA Within The Nucleus' was published on July 19, 2006. The italicized article appears below along with my comments in standard print.

DNA – the long, thin molecule that carries our hereditary material – is compressed around protein scaffolding in the cell nucleus into tiny spheres called nucleosomes. The bead-like nucleosomes are strung along the entire chromosome, which is itself folded and packaged to fit into the nucleus. What determines how, when and where a nucleosome will be positioned along the DNA sequence? Dr. Eran Segal and research student Yair Field of the Computer Science and Applied Mathematics Department at the Weizmann Institute of Science have succeeded, together with colleagues from Northwestern University in Chicago, in cracking the genetic code that sets the rules for where on the DNA strand the nucleosomes will be situated. Their findings appeared today in Nature.

The precise location of the nucleosomes along the DNA is known to play an important role in the cell's day to day function, since access to DNA wrapped in a nucleosome is blocked for many proteins, including those responsible for some of life's most basic processes. Among these barred proteins are factors that initiate DNA replication, transcription (the transfer of genetic information from DNA to RNA) and DNA repair. Thus, the positioning of nucleosomes defines the segments in which these processes can and can't take place. These limitations are considerable: Most of the DNA is packaged into nucleosomes. A single nucleosome contains about 150 genetic bases (the "letters" that make up a genetic sequence), while the free area between neighboring nucleosomes is only about 20 bases long. It is in these nucleosome-free regions that processes such as transcription can be initiated.

Gene regulation takes many forms. This type involves a physical barrier designed to inhibit the expression of genes. The idea is to utilize nucleosomes to deny protein access DNA. This in turn inhibits the transcription of particular proteins as well as the functions they are associated with. Allowing gene expression through further movement of nucleosomes is of course also possible.

For many years, scientists have been unable to agree whether the placement of nucleosomes in live cells is controlled by the genetic sequence itself. Segal and his colleagues managed to prove that the DNA sequence indeed encodes "zoning" information on where to place nucleosomes. They also characterized this code and then, using the DNA sequence alone, were able to accurately predict a large number of nucleosome positions in yeast cells.

DNA sequences are then tied to gene expression through their effects on nucleosome placement.

Segal and his colleagues accomplished this by examining around 200 different nucleosome sites on the DNA and asking whether their sequences have something in common. Mathematical analysis revealed similarities between the nucleosome-bound sequences and eventually uncovered a specific "code word." This "code word" consists of a periodic signal that appears every 10 bases on the sequence. The regular repetition of this signal helps the DNA segment to bend sharply into the spherical shape required to form a nucleosome. To identify this nucleosome positioning code, the research team used probabilistic models to characterize the sequences bound by nucleosomes, and they then developed a computer algorithm to predict the encoded organization of nucleosomes along an entire chromosome.

The team's findings provided insight into another mystery that has long been puzzling molecular biologists: How do cells direct transcription factors to their intended sites on the DNA, as opposed to the many similar but functionally irrelevant sites along the genomic sequence? The short binding sites themselves do not contain enough information for the transcription factors to discern between them. The scientists showed that basic information on the functional relevance of a binding site is at least partially encoded in the nucleosome positioning code: The intended sites are found in nucleosome-free segments, thereby allowing them to be accessed by the various transcription factors. In contrast, spurious binding sites with identical structures that could potentially sidetrack transcription factors are conveniently situated in segments that form nucleosomes, and are thus mostly inaccessible.

Since the proteins that form the core of the nucleosome are among the most evolutionarily conserved in nature, the scientists believe the genetic code they identified should also be conserved in many organisms, including humans. Several diseases, such as cancer, are typically accompanied or caused by mutations in the DNA and the way it organizes into chromosomes. Such mutational processes may be influenced by the relative accessibility of the DNA to various proteins and by the organization of the DNA in the cell nucleus. Therefore, the scientists believe that the nucleosome positioning code they discovered may aid scientists in the future in understanding the mechanisms underlying many diseases.

The disruption of nucleosome function is implicated as a likely source of some diseases and cancer. One of the better news stories to come along in quite some time.

Thursday, July 27, 2006

Denyse O'Leary

Journalist and author Denyse O'Leary, who now co-hosts the weblog 'Uncommon Descent' with William Dembski, recently posted an entry at her blog Post Darwinist which made mention of this blog. From the entry in italics.

Roll on, blogs, roll on: Never be bored!

The blogroll at the side features three new never-be-bored entries.

Intelligent Sequences, featuring William Bradford, currently unpacking the Darwin legend as breathlessly reported in the faith and science media.

Thanks for the comment. Denyse's blog can be accessed at:

Denyse's book 'By Design or by Chance?' filled a vacuum by making available information about intelligent design to the general public. A website features the following book critique:

What the experts are saying about By Design or by Chance? The Growing Controversy on the Origins of Life in the Universe:

“O'Leary provides by far the broadest popular overview yet of the ID movement. She quotes ID leaders such as Phillip Johnson, William Dembski and Michael Behe. She also quotes their sternest critics, including Richard Dawkins, Stephen J. Gould and Michael Ruse. She writes about the Wedge Movement, DNA, the age of the Earth, the search for extraterrestrial life, the teaching of ID in schools, and the monarch butterfly. She anticipates the culmination of the ID revolution by writing that Darwinism ‘was part of our folklore.’ Yet the evolutionary tales she relates are still widely taught as fact in many schools.

This well-organized guidebook of O’Leary’s journey through the world of Intelligent Design has the potential to lead many of the next generation away from the evolutionary fables that now pass for science. Her book is must reading for anyone who wants to understand the history and significance of the Intelligent Design movement. It also belongs in college and even high school classrooms.”
Forrest M. Mims III

Since the first book Denyse has written 'Faith@Science: Why Science Needs Faith in the 21st Century.'

Wednesday, July 26, 2006

Arriving at a Conclusion Should be a Process

This is from an Uncommon Descent post.

Wesley Elsberry, in blogging about Denyse O’Leary’s recent coming on board here at UD, refers to her as a “pseudo-journalist” (go here)? What a curious designation. Does Wesley’s use of the prefix “pseudo” simply indicate his disapproval of O’Leary and, in particular, her failure to accept his brand of evolution? Or does the prefix indicate something substantive (Denyse, did you come on board here under false pretenses? Are you really a journalist at all? What exactly have you published in recognized media outlets?)

If Denyse is in fact a real journalist, does that make Elsberry a “pseudo-blogger”?

And the following comment and response to the comment from Austringer's blog Comments italicized. Denyse's remarks in bold print.

What do you mean, she pouts if you call her an ID advocate?

Austringer Says:
July 20th, 2006 at 5:05 am
Maybe she’s given it up recently, but for several years whenever she was called an ID advocate, her response was that she was an objective journalist and not an advocate of anything.

Given Denyse's journalistic history the above statement exactly describes a period of time in her life. Her arrival at an ID point of view was the result of a process of investigating the evidence pertinent to the controversy. Actually there should have been a point in time in all of our lives when we could have stated that we were not an advocate for evolution or ID until... If that was not the case for Wesley Elsberry then why not? Wasn't it an objective assessment of scientific data that led him to his own convictions and if that is so, was there not a time prior to his familiarity with the evidence that he would have truthfully said he was not an advocate for evolution? Now Wesley, don't tell us you were an advocate before becoming familiar with the evidence. Is that the case? It appears either there was a time when you, like Denyse, were not an advocate or you were an advocate before familiarizing yourself with the facts necessary to make an intelligent decision. Which is it Wesley?

Consider her response from this interview:

There are lots of books attacking evolution or advocating for intelligent design (ID)—such as Darwin on Trial or The Case for a Creator. What’s different about your book?

By Design or by Chance? wasn’t written to attack evolution or to advocate intelligent design. It was written to explain what all the shouting is about. It is aimed at a general audience, not necessarily a Christian one. In 1996, a political science prof based in Toronto urged me, as a journalist, to address the unseemly and unscholarly attacks on mathematician David Berlinski, for daring to question Darwinism. I ended up writing a book. In the course of writing, I came to the conclusion that intelligent design is more plausible than Darwinism, as an explanation for the life we see around us. By Design or by Chance? is not written to advocate Christianity. I am a traditional Christian, but I recognize that most faiths represented on this planet can account for intelligent design. Only atheistic secularism cannot. The question must be decided on evidence.

Sounds like a reasonable approach. Evaluate the subject matter before coming to a conclusion. So what's wrong with that Wesley?

Tuesday, July 25, 2006

Evolution According to Ruse: Part Two

This is the second post on Michael Ruse's article entitled 'What Darwin's finches say of Creation.' Parts of Ruse's article appear in italics. My comments are interspersed throughout the piece.

And now, as reported in the Tallahassee Democrat, there is direct evidence of evolution in Darwin's finches.

This claim has been exposed for the 'Darwinian Hyperbole' that it is. From the cited article:

"Why a journalist might think this constitutes evolution is not hard to understand. What is difficult to grasp is why a scientist would call it evolution. There's no speciation involved here, no reproductive isolation, no indication of an alteration in the finch's genome, no "different sort of animal," just a simple modification of the size of an anatomical structure triggered, apparently, by the unavailability of a particular food source.

This is only evolution if evolution is defined in such a way as to include any variation that occurs in a population of organisms, but such a definition renders the concept meaningless."

These are the little birds to be found on the Galapagos Archipelago, on the equator in the Pacific. In the past 20 years, one species of the finch on one of the islands (Daphne) has moved in the direction of much smaller beaks. The reason is that another species invaded the island. This new species is much better at cracking and opening large seeds, and so the original group has now started to specialize on very small seeds.

What makes this latest finding very exciting is that the process whereby the finches are gaining smaller beaks - those that have smaller beaks get fed and survive and reproduce, and those with bigger beaks do not - is a classic example of the mechanism of natural selection. This is the idea first proposed by Charles Darwin in his "Origin of Species" in 1859, And what makes the finding doubly exciting is that it was these very Galapagos finches (and the mockingbirds, also to be found on the islands) that made Darwin into an evolutionist.

This invocation of natural selection as applicable to all genetic changes was addressed in the prior post on this article. It is an apples to oranges analogy that Ruse is entitled to as a matter of opinion however the types of genetic changes required to engender a transition to the eukaryotic genome of a finch is simply not documented as even theoretically analogous to what we see among these finches.

There are 13 species of finch on the islands. Darwin argued that the only explanation is that a founder population of birds arrived on the Galapagos and then evolved as they hopped from one island to another.

Unfortunately, those of us who love evolutionary ideas - who think that puzzling out the past is the best possible proof that we are more than just modified monkeys and may even be made in the image of God - know full well that the majority of Americans will reject this wonderful science, and will feel that the judge in Pennsylvania made the wrong decision.

People do not reject scientific data. They reject unwarrented extrapolations drawn from such data. The finch finding is evidence that an adaptation has occured within a species. It is not evidence that the ancestral line of these finches extends to a unicellular organism that arose in prebiotic earth conditions. Evidence for that type of transformation requires substantially different evidence as was pointed out in part one of this two part posting.

More people believe in the six days of Creation, that the earth is less than 10,000 years old, and that humans lived alongside dinosaurs, than believe that the universe is 15 billion years old, that the earth is 4.5 billion years old, and that life has been around for more than 3.5 billion years. More people believe the Hebrew myths of Genesis than that God could show his power and his glory with the wonderful unfurling process of evolution.

Genesis covers more than creation. There is much evidence that alleged myths are historic facts. If Ruse is confining his myth tag to the creation account then why bother to go on to state that Christianity "has always had in it the power and necessity to interpret the Bible metaphorically"? Having set up a means to evaluate Genesis differently from the "literalists" he then surprisingly rambles about "Hebrew myths of Genesis." What distinguishes a myth from a metaphor and how would you know Michael Ruse? How does Ruse decide which parts of Christianity to take seriously and which are myths? Or is this reference to metaphors a bone he holds out to fence sitters?

More people want to ignore the real truths of Genesis - about God as Creator and about our special relationship to him - and want to embrace some cramped little fable from pre-Christian storytelling.

Aha. The Genesis author coopted the creation account from another prior account. I've run across this before. Supporting evidence is weak but more importantly there is no reason to conclude that one who believes that life was generated through a direct act of divine power is thereby ignoring the real truths of Genesis. This type of assertion is unworthy of one with Ruse's academic crdentials.

The cry will go up that people like me - people who think you can be an evolutionist and equally be a sincere Christian or Jew or Muslim (or whatever) - are simply wrong. It will be said that we ignore traditional religion and embrace some newly fabricated, modern illusion. This is simply not true. Christianity (to speak of just one religion) has always had in it the power and necessity to interpret the Bible metaphorically, if the science dictates. St. Augustine, around 400 A.D., insisted that the Bible is written in the language of primitive folk and that we who come later must interpret it according to the knowledge of our day. I am not saying that Augustine himself was an evolutionist - although as it happens, since he believed that God stands outside time, he did think that God created seeds of life that then develop. I am saying that traditional religion demands that we use that which makes us in God's image, namely our powers of sense and reason.

So let us celebrate the findings of science. Darwin's finches are drab little birds, living on outcrops of hot, inhospitable, volcanic rock, in the middle of the ocean. But they tell us more about the wonderful world in which we live, and of our powers of understanding, than do years of misguided poring through the leaves of the early chapters of the Old Testament.

What happended to "the real truths of Genesis - about God as Creator and about our special relationship to him"? Make up your mind Professor Ruse. Darwin's finches tell us that the finch genome has the capacity for beak size adjustment. Extrapolations extending well beyond this are not in the interest of science.

Monday, July 24, 2006

Evolution According to Ruse: Part One

Take a look at this article entitled 'What Darwin's finches say of Creation' if you want a glimpse at issues underlying the struggle between proponents of intelligent design and evolution. As stated at the end of the article "Michael Ruse, the author, "is the Lucyle T. Werkmeister professor of philosophy at Florida State University and an authority on the history and philosophy of science." Frankly, it is astounding that someone with his credentials makes the basic blunders evidenced by this article. The first part of this article appears in italics. My comments are interspersed throughout the piece. A second post will examine the remainder of the article.

By Michael Ruse

This has been a good year for evolutionists. First, at the end of 2005, a judge in Pennsylvania - a conservative appointed by President George W. Bush - decreed that so-called Intelligent Design Theory is not genuine science and hence cannot be taught in publicly funded science classrooms.

Intelligent Design Theory - Creationism Lite - is the latest attempt by religious fundamentalists, biblical literalists, to argue that the origins of organisms were not evolutionary but the result of injections of divine power.

Here is a mischaracterization. Advocates of intelligent design are not limited to those who are "biblical literalists" to quote the author. They include those with differing biblical interpretations as well as prominent non-Christians like David Berlinski who is Jewish and Mustafa Akyol; a Muslim. Included also are many individuals, of a variety of faiths, who are not well known. In that respect it is very much like evolution.

In other words, God was not prepared or able to let things unfurl naturally according to unbroken law, but got directly involved through miracles.

This is a theological argument and a poor one at that. But if it is theological points Michael Ruse wishes to consider then, if the origin of life can be traced to unknown chemical reactions, why did God conceal the evidence for it? Before genetic changes can occur a genetic code and ordered nucleic acid sequences must first exist. How does this come about through extra-cellular organic chemical reactions? Before deciding that something unfurled according to unbroken law why not specify the empirical evidence showing the pathway from prebiotic conditions to a living cell, Professor Ruse? Why invoke a miracle and call it abiogenesis instead?

The judge rightly ruled that this is not science, it is religion, and violates the Constitution's separation of church and state.

Judge Jones will not determine the outcome of this historic struggle. He's a blip on the screen. Ideally we should be focused on scientific evidence not legal edicts or theological arguments. The separation clause is the most abused legal concept in America. Justified based on selected views of particular founding fathers, primarily Thomas Jefferson as gleaned from a private letter he wrote, the concept has been misused to muzzle views not to the liking of a segment of American society. The founding fathers wanted to avoid the Cromwell experience of Great Britain. They envisioned a government that would not impose a particular religion on America. Intelligent design argues that an intelligent cause best explains evidence associated with natural history. It distinctly repudiates the idea that any particular religious group be endorsed by the movement. William Dembski is not validated because of his Christian views at the expense of David Berlinski or Mustafa Akyol. IDers are identified by their belief in intelligent causality not Christianity, Islam, Hinduism, Judaism...

Then from the snowy wastes of northern Canada came reports of fantastic new fossils. Paleontologists from the University of Chicago found forms midway between fish and amphibians. These finds are as exciting as the famous Archaeopteryx, the bird with reptile-like features (small brain, separate fingers, and so forth) or, if you prefer, the reptile with feathers. This newly discovered fish-reptile is christened Tiktaalik, the Inuit name for large, shallow-water fish. It lived in water but had adaptations to make frequent trips out to the dry land. It is precisely what one expects if evolution is true.

The focus has arrived where it should be- the physical evidence. Evolution requires transition states and one would expect to find them in the fossil record. Ruse is pointing to a fossil that could be argued as just such a transitional species. Since the fossil record also shows the sudden appearance of organisms without transitional fossils, the finds identified by Ruse are welcomed by evolutionists.

There is of course more to scientific evidence and recent finds. Here is a hot one right off the griddle.

'Scientists Say They’ve Found a Code Beyond Genetics in DNA'

"Researchers believe they have found a second code in DNA in addition to the genetic code.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell."

Also another perspective on the same discovery: 'Scientists Discover a Genetic Code for Organizing DNA':

"The team’s findings provided insight into another mystery that has long been puzzling molecular biologists: How do cells direct transcription factors to their intended sites on the DNA, as opposed to the many similar but functionally irrelevant sites along the genomic sequence? The short binding sites themselves do not contain enough information for the transcription factors to discern between them. The scientists showed that basic information on the functional relevance of a binding site is at least partially encoded in the nucleosome positioning code: The intended sites are found in nucleosome-free segments, thereby allowing them to be accessed by the various transcription factors. In contrast, spurious binding sites with identical structures that could potentially sidetrack transcription factors are conveniently situated in segments that form nucleosomes, and are thus mostly inaccessible."

What observable evidence do we have indicating that a second genetic code would result from selected mutations? We have yet to find a force of nature identified as the cause of the original genetic code. The Darwinian mutation mechanism is a modifying not a generating effect i.e. the existence of an encoding system is postulated and changes to it theorized. Origins issues are associated with weak supporting empirical evidence. The news of a possible second code appears to fit within an evolutionary time frame so how does the evidence stack up for it?

Evolution is said to have occurred through changes that became fixed in populations as a result of natural selection. Natural selection was used by Darwin to explain how species evolved. It was a logical argument when introduced and empirical data supporting the concept is still wanting. Bacterial adaptation is well known and perhaps the most commonly cited example of environmentally induced genetic changes. What is not generally appreciated is both the nature of such genetic changes and the nature of genetic changes alleged to have been engendered by an evolutionary process about which extrapolations from unicellular adaptations are used as evidence for the theory.

Observable events involving selected genetic changes have been limited in their scope. They are not observations of new multi-protein systems evolving, but rather are limted almost entirely to changes in already existing systems resulting from single mutations events. The discovery previously cited is identified with specific DNA sequences and nucleosomes. But just as there is more to the letters in your newspaper than the ink composing them, it is likewise the case with genetic codes. The selective value of the code lies in its regulatory effects. The genetic mechanism associated with the shortening and lengthening of bird beaks are simple. The alleles connected with these traits already exist in bird genomes. By contrast there is no historic precedent involving observation of the kind of genetic change required to generate eukaryotic genomes characterized by nucleosomes and encoded signals.

There are encoded signaling systems known to scientists but they are the products of intelligence. They also have a common property namely, the insufficiency of forces of nature to explain the sequential order of the constituent encoding symbols which in this case entails both nucleotides and nucleosomes (themselves encoded end products) having shielding functions. Symbolic encoding conventions, if found outside biological systems, (even in a different part of this universe) would be assumed to be of intelligent origin. The contention that biological systems are different because Darwin showed that natural selection demonstrates unintelligent pathways to biological phenomenon is erroneous. At best it explains restricted circumstances. At worse it is an example of misusing language to argue false analogies. The genetic dynamics associated with changing beak sizes are altogether different from that required to realize the evolution of a nucleosome code and eukaryoric genomic features. Calling both examples of natural selection expresses a personal opinion not an empirically documented argument. Insisting that both phenomenon are comparable and leaving it at that reveals either ignorance, deliberate deception or ideological blindness.

Saturday, July 22, 2006

Solving Puzzles

Research news from the Howard Hughes Medical Institute in an article entitled 'Joining Hands to Solve a DNA Replication Puzzle' provides a good description of viral dynamics in the form of interaction between viral proteins and cellular replication protein A (RPA) which has a protective function related to ssDNA (single-stranded DNA). As the author indicates RPA is involved in replication and repair pathways both of which have important implications for intelligent inferences. From the italicized article:

Every organism has an ssDNA-binding protein for DNA replication and repair pathways. In eukaryotes or organisms whose cells have a nucleus, it is called replication protein A (RPA). One of the common functions of RPA in DNA processing pathways is facilitating “hand-off,” a process that ensures that the correct proteins move into place along the ssDNA to begin DNA processing.

RPA plays an important protective role for ssDNA. “You don't want to have naked single-stranded DNA lying around in a cell,” explained Fanning. “It will get tangled, make hairpins within itself, get chewed up by nucleases. Ss binding proteins keep ssDNA straight and accessible to the right processing enzyme.”

RPA binds with at least a dozen different repair and replication proteins. The question has been how RPA gets dislodged, allowing various enzymes access to the DNA for necessary processing. Fanning and Chazin have developed a working model to answer that question.

Using SV40 as a model system, the scientists mapped atomic level interaction on the surfaces of proteins involved in DNA processing. They used biochemical and genetic tools to determine how the interactions of those proteins promote synthesis of small segments of RNA known as primers, which are required for initiation of DNA replication.

In the SV40 system, three key proteins interact. The viral protein T antigen (Tag) interacts with RPA and an enzyme known as DNA polymerase-primase (pol-prim). Tag is a helicase, or DNA unwinding enzyme. After it has unwound the DNA, it also places the pol-prim on the DNA to make primers. The researchers studied this last step: how Tag pulls RPA away sufficiently to load the pol-prim onto the DNA, allowing it to synthesize primers.

Fanning and Chazin showed that interaction between Tag and RPA requires multiple contact points. They found that, along with a domain on RPA called RPA70, a second one, RPA32C, also needs to bind to Tag before processing can begin.

The scientists suggest that Tag associates first with RPA32C and then with RPA70 as the RPA molecule sits on ssDNA. Binding at both of these points alters the conformation of RPA, scrunching it up to expose a small stretch of ssDNA. Tag brings with it pol-prim, which is deposited in the short stretch of unbound ssDNA. Once pol-prim is in place, Tag and RPA are no longer needed, so they are displaced as the third protein begins its work on the ssDNA. This is the “hand-off.”

How would viruses like SV40 come into existence? The functional value of their proteins is clear as is the need for a host. Interaction with a host entails interaction with specific proteins of that host. How would a natural selection process explain how and why the viral genome came about?

Friday, July 21, 2006

Darwinian Propaganda

The Viewpoint section of the website featured an on-target critique of a recent article claiming that evolution had been observed in finches. The following italicized part was taken from 'Darwinian Hyperbole.'

Why a journalist might think this constitutes evolution is not hard to understand. What is difficult to grasp is why a scientist would call it evolution. There's no speciation involved here, no reproductive isolation, no indication of an alteration in the finch's genome, no "different sort of animal," just a simple modification of the size of an anatomical structure triggered, apparently, by the unavailability of a particular food source.

This is only evolution if evolution is defined in such a way as to include any variation that occurs in a population of organisms, but such a definition renders the concept meaningless.

Exactly. This trivializes biology.

The amusing and disingenuous ploy at work in reports such as this is that they are used to support the claim that evolution is a fact.

In other words we are witnessing a ploy at promoting Darwinism.

Darwinists will argue that evolution (meaning molecules to man evolution) is as firmly established as gravity, that anyone who questions it is either ignorant or malicious, but when the public meekly requests a crumb of evidence to support that claim it's shown pictures of finches with diminished beaks. We may as well be told that since humans, because of better nutrition, have grown taller in the last century and a half, and live longer, evolution is therefore a fact.

Equating abiogenesis and evolution with laws of physics that are precisely defined and have been tested and verified repeatedly is the real indicator of either ignorance or maliciousness.

Tuesday, July 18, 2006

Statement of Belief or Evidence for it?

An article from Biocompare entitled 'Evolution Reveals An Independent Route For Diversity In Animal Form' reveals an interesting discovery and some can't miss promotion strategy on behalf of evolution. A part of the article appears in italics along with some comments.

"Researchers have found that Cnidaria, a group of marine animals noted for diverse morphology among its constituent species, actually lacks the ancient "Hox" gene system that is essential for the development of most other animals. The finding is surprising because the Hox system is largely responsible for so-called axial patterning, the developmental process that directs the formation of different morphological features along the anterior-posterior axis--the axis along which the head, trunk, and tail are arranged. The work indicates that despite the importance of the Hox system in the development of most animals, the evolution of a typical Hox system is not in fact a prerequisite for axial patterning during development or for the generation of diverse animal morphology.

The findings are reported in the May 9th issue of Current Biology by scientists Bernd Schierwater, Kai Kamm, and Wolfgang Jakob of Tierärztliche Hochschule Hannover, in Germany, Stephen Dellaporta of Yale University, and David Miller of James Cook University in Australia.

A remarkable feature of Hox-system genes is that they are typically clustered in groups along chromosomes, with their order along the chromosome reflecting their actual pattern of expression along the anterior-posterior axis of a developing animal. The Hox system has long been considered a defining characteristic of animals, and much of the variation seen in animal morphology has been attributed to evolutionary variations on how the Hox system is implemented during development in different species."

The hox system, in all its variations, is considered to be the result of an evolutionary process. It is believed to have evolved and then been passed down from generation to succeeding generation. Note the title again. Who revealed the independent route? None other than evolution. Variations, or even entirely different biological systems, are always credited to evolution even when the writer or researchers have no clue as to how variation occured. Constant exposure to these types of articles can lead an unwary reader into thinking evidence for evolutionary claims is stronger than it actually is. Actually these kinds statements are more declarations of belief than demonstrations of scientifically supported assertions.


Chuck Colson's article entitled 'Worshipping the Goddess of Tolerance' contains some insightful comments about tolerance; a modern western scourge. The two following paragraphs are taken from the article.

"Dorothy Sayers, the great English writer, said it best: “In the world it is called Tolerance, but in hell it is called Despair, the sin that believes in nothing, cares for nothing, seeks to know nothing, interferes with nothing, enjoys nothing, hates nothing, finds purpose in nothing, lives for nothing, and remains alive because there is nothing for which it will die.”

This kind of so-called “tolerance” can never bring people together, but only as we saw in Washington, pull them farther apart."

As the noted evolutionist Stephen Jay Gould once pointed out there are value issues that transcend disputes over natural history. Evolutionists who dig in their heels and insist that the world accept an origins paradigm that excludes intelligent causality show that they have beliefs. However those among them who consider tolerance a supreme virtue suffer from the same moral paralysis afflicting those mentioned in the Colson article. It is difficult to formulate coherent value based policies when differing factions in the big tent must all be accomodated. Mediocrity and indecision result.

Sunday, July 16, 2006

Teaching Natural History

Frequently asked questions and answers from the website 'Teach Darwin Honestly.' Efforts to reform our educational system's approach to the teaching of natural history will not fade away despite the best efforts of Judge Jones and his ilk. Changes should entail the inclusion of a more accurate presentation of scientific evidence. This does not favor the status quo but since when has maintaining that been associated with progress? In italics from the cited website:

Q: How have the Standards improved?
A: The New Standards:
• reflect updated science
• promote informed decision making
• contain more specific teaching objectives formatted to facilitate assessment.
• Seek objective teaching of the scientific controversy over evolution.
• Urge teachers to reinforce normative parental and legal expectations about health issues.

Q: What is the scientific basis for the changes?
A: Most of the changes reflect common sense and all have a solid scientific basis. They were crafted by eight members of the Writing Committee (the Authors), three of which hold doctoral degrees in the life sciences (biochemistry, entomology and medicine). They were then scientifically and educationally validated by 23 experts during 3 days of hearings in May, 2005 by 5 PhD biologists/molecular biologists, 4 PhD biochemists, 3 PhD Chemists (2 with expertise in theories of chemical evolution - origin of life), 1 PhD Geneticist (the inventor of the Gene Gun), 1 PhD Quantum Physicist, 3 Philosophers of Science (two with PhD’s), 1 PhD Professor of Education, 3 biology teachers, a Muslim journalist and an attorney.

Q: How do parents want evolution taught?
A: Parents want evolution taught honestly. Most Polls conducted by highly regarded organizations show that more than 80% of the public oppose an “evolution only” curriculum, i.e., one that discourages critical analysis of evolution.

Q: Did the Board insert Intelligent Design into the standards?
A: No. It expressly excluded ID from the standards.

Q: Did the Board remove evolution from the standards as stated by the National Association of Biology Teachers (NABT)?
A: No. This is misinformation that seeks to suppress any critical analysis of evolution.

Q: Why has the Board opened Pandora’s box by inserting discussions of “origins” into the standards?
A: The Board did not insert origins. It inserted objectivity into an existing one-sided discussion of origins. Textbooks and prior science standards teach the origin of the universe and the origin of life and its diversity from a single perspective. The new standards are more objective.

Q: Are the changes educationally appropriate? It has been argued that many biology teachers will disregard them.
A: Yes. They seek objective discussions of origins that are less stressful for students and teachers. Teachers testified that they are afraid to teach origins objectively because of pressure from institutions of science and education. Professor Warren Nord argued that a liberal education requires teaching both sides of controversial issues.

Q: Why is the teaching of origins so controversial?
A: It is scientifically controversial because it is an historical science, and therefore very subjective. It is religiously controversial because it addresses the question: “Where do we come from?” This is a question that some claim is inseparably linked with the question: “Where do we go?”

Q: Do the changes seek to criticize evolution to advance religion?
A: No. They seek to eliminate rather than advance a religious bias that permeated the old standards.

Q: Are the changes legal? It has been argued that they insert religion into the standards.
A: Yes, they are legal. They insert scientific objectivity rather than a bias that favors a particular religious perspective.

Q: Will the changes drive businesses out of Kansas and disqualify students for college?
A: No. This is propaganda designed to frighten rather than inform. It amounts to crying “FIRE! FIRE!” in a crowded theater when there is no fire. This deception was concocted by founders of Kansas Citizens for Science and was outlined in the November 2000 issue of Freethought Today, a publication of atheists and agnostics.

Q: Why do we get conflicting reports about the changes to the standards?
A: Organizations that oppose the changes are unwilling to publicly debate evolution because they falsely claim it is not scientifically controversial. To avoid a discussion of the real controversy they unfairly demean those who seek it. See for an explanation of the strategy of the media and public relations officer of Kansas Citizens for Science: our “strategy" is to "portray” those who seek an objective discussion of evolution “in the harshest light possible, as political opportunists, evangelical activists, ignoramuses, breakers of rules, unprincipled bullies, etc.” The boycott of hearings that discussed the key issues of science and education is an example of this strategy - to demean rather than to discuss.

Q: How do the 2001 and 2005 definitions of science differ?
A: The 2005 definition replaces a novel definition of science (not found in other state standards or the national standards) with this traditional definition:

“Science is a systematic method of continuing investigation, that uses observation, hypothesis testing, measurement, experimentation, logical argument and theory building, to lead to more adequate explanations of natural phenomena.” [The definition continues for two more paragraphs that increase, rather than decrease the scientific rigor of this concept.]

Q: Does the 2005 definition redefine science?
A: No. It is a traditional definition that is consistent with other state science standards and the National Science Standards. It is rigorously objective and focused on empiricism. It derives from the Ohio Academy of Science definition, and is consistent with the definition embraced by the US Supreme Court.

Q: Doesn’t the new definition imply that Kansas will now seek supernatural causes?
A: No. By describing science as an open-ended search for more adequate or reliable explanations of the natural world using empirical methods, it implies nothing about the supernatural.

Q: What changes did the Board make about origins and evolution?
A: The following reflect most of the key changes:

• Added a reminder to teachers that: “Although science proposes theories to explain changes, the actual causes of many changes are currently unknown (e.g. the origin of the universe, the origin of fundamental laws, the origin of life and the genetic code, and the origin of major body plans during the Cambrian explosion).”

• Added an indicator about the evaluation and testing of historical claims, a concept important not only to origins, but also to geology, paleontology, archeology, and forensic sciences.

• The Board added material that more completely describes the core postulates of evolutionary theory, so that students will know that “Biological evolution postulates an unguided natural process that has no discernable direction or goal....” with new traits arising “from new combinations of genes and from random mutations or changes in the reproductive cells.”

The Standards introduce students to major scientific controversies about:

• Universal common ancestry.

• The adequacy of evolutionary mechanisms, that are known to produce micro changes within a species, to also explain macro changes such as “new complex organs or body plans and new biochemical systems which appear irreducibly complex.”

• Chemical explanations for the origin of life.

Detecting Viral RNA

A Biocompare news article entitled 'Immune System Response To Viral DNA Is Unique' discusses recognition of foreign DNA; a vital function in defending against viral as well as bacterial pathogens. Some comments follow. Passages from the referenced article appear in italics.

Although there are countless types of viruses, they can all be placed in two categories based on the type of nucleic acids that comprise their genome: viruses made of RNA and viruses made of DNA. Infected cells sense the presence of foreign nucleic acids as viruses replicate inside them and distill the problem of recognizing a dizzying array of viruses into a relatively simple mechanism for turning on the immune response.

"It is well established that such a pathway exists for detection of viral RNA inside infected cells," Stetson said. "In contrast, very little is known about whether cells can detect foreign intracellular DNA or how this system might function."

Different detection pathways, in addition to other factors, might explain pathogen dynamics. For example, RNA viruses that utilize the reverse transcription process can be classified into distinct families. Retroviridae are associated with vertebrates, metaviridae with fungi and invertebrates and pseudoviridae with invertebrates. Variation in cellular mechanisms that distinguish between different types of RNA offer intriguing explanatory possibilites.

"We found that this novel pathway seems to function differently from all other known nucleic acid sensors," Stetson said. "The unique immune response activated by foreign DNA suggests that DNA viruses and RNA viruses are detected by different mechanisms."

Stetson said one important question raised by these findings is how this newly described system avoids responding to genomic DNA that is contained within all cells.

"If this 'tolerance' to self DNA were to break down, cells might mount an antiviral response against their own DNA," he said. "Further characterization of this pathway will shed light on the mechanisms of antiviral responses and how cells discern viral and self-DNA."

Malfunction involving nucleic acid detection mechanisms could indeed be linked to diseases whose causes are still unknown.

Friday, July 14, 2006

Recognizing Evidence for Intelligent Design

A post entitled 'Reliable Recognition of an Intelligent Agency' sparked some comments in reaction to it. The post appears at this blogsite. An exchange involving me and another commenter is included. My comments are italicized.

Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?

Why should intelligence possess such properties? The only reasons I can see relate to the efficiency of certain approaches.

Then let me suggest another. Intelligence is detectable in the very nature of this exchange. It is possible to generate the alphanumeric symbols through a source unfamilar with English language encoding conventions but the result will be nonsense. Pets, inanimate objects and toddlers all have key compression capacity. They lack a capacity to generate intelligible messages. A biological counterpart is nucleic acids whose biological utility is a function of their sequential order. Rearranging the codon order of a functional DNA molecule will negate its function without changing its chemical nature. Function is not dependent on chemical identity which is the same for both functional and non-functional nucleic acids. It is related to their selective value; problematic in generating an initial genome, in the absence of intelligence, on prebiotic earth.

Common properties of similar entities can be intelligently inferred through inductive reasoning and recognized deductively.

Except that our sample size is very limited - we only really have one intelligence to examine. Attempting to make an inference based on that is therefore going to run into more or less unavoidable difficulties due to lack of data.

We have a broad array of intelligent capacity and examples of its expression upon which inferences can and have been made. Our sample size of genetic information carriers known to biology is limited to nucleic acids. Not a problem. You analyse what is before you.

This type of approach is common in science. Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?

Well, firstly you'd have to come up with a rigorous test for "analytical or abstract thought". Then you'd have to check that there could be no false positives (this would presumably be accomplished by mathematical means).

The test entails the capacity of an unguided natural force to generate the sequential order of symbols in conformity with the code at hand to express either this message or the gene expression required of a functional genome.

Thursday, July 13, 2006

Detecting Intelligence

The title and first paragraph are from one of Dembski's blog entries. My comments are in italics.

'Detecting Design — that’s not science; Detecting Intent — that’s science'

"How is it that when cognitive psychologists and computational intelligence engineers detect user intent, they are doing science, but when ID theorists detect design in biological systems, they aren’t? There’s a double standard here. ID might fail as a science — methods of design detection might be defective or fail to yield a positive result, but to say that their application does not even constitute science, as Judge John E. Jones III ruled in Kitzmiller v. Dover, is on its face ludicrous. Consider the following letter from a colleague:"

If their application does not constitute science then a decision has been made in advance that purely natural forces (devoid of evidence of intelligent input) are capable of generating desired outcomes. Judge Jones did what every clever evolutionist does- ignore the weakest link in their chain of evidence. Pretend that a case exists in favor of evidence for the origin of life, which on the face of it, excludes rational consideration of intelligent causality. Talk about evidence for evolution and consider abiogenesis the embarrassing step-child to be avoided in polite conversation. Abiogenesis is relegated to a separate area of study enabling evolutionists to claim that evidence for it may be inadaquate but we will find it eventually. In the meantime let's discuss common descent. It's an article of faith on their part not to be confused with solid scientific evidence.

An intelligent inference can be made at any point in the process. Take heed Judge Jones and your fans.

Is Evolution Cleverer than You?

An article entitled 'Putting the Cart Before the Horse' uses a passage from a speech of Daniel Dennett, atheist and Darwinist, as a basis for commentary. Parts of the article appear here in italics.

Francis Crick called Orgel's Second Rule. "Evolution is cleverer than you are."

Again and again evolutionists, molecular biologists, biologists in general, see some aspect of nature which seems to them to be sort of pointless or daft or doesn't make much sense - and then they later discover it's in fact an exquisitely ingenious design - it is a brilliant piece of design - that's what Francis Crick means by Orgel's Second Rule.

This might almost look like a slogan for Intelligent Design theory. Certainly Crick was not suggesting that the process of evolution was a process of intelligent design. But then how can evolution be cleverer than you are?

What you have to understand is that the process itself has no foresight; it's entirely mechanical; has no purpose - but it just happens that that very process dredges up, discovers, again and again and again, the most wonderfully brilliant designs - and these designs have a rationale. We can make sense of them. We can reverse-engineer them, and understand why they are the wonderful designs they are.

This is an argument by assertion. A purposeless, mechanical process devoid of foresight is not only clever but more so than you are. How do we know? It's our capacity to discover and make sense out of "wonderfully brilliant designs." Incidentally, this thought process plays out over and over again in articles citing results of various scientific studies. Notice how often the discussion of scientific data is accompanied by a speculative expression attributing evolution as a cause related to the data in question. There is no need to show a detailed linkage. The underlying assumption that a purposeless, mechanical force was at work is sufficient.

It's hard to read this without getting the feeling that Dennett is trying with all his might not to admit that living things certainly appear to be intelligently designed. Indeed, were it not for Dennett's a priori committment to atheism he would probably not even bother to engage in such a laborious struggle. He gives the game away in this paragraph where he tries to convince us that a blind, mecahnical process is even more brilliant, more ingenious, than the most clever of human engineers:

What you have to understand is that the process itself has no foresight; it's entirely mechanical; has no purpose - but it just happens that that very process dredges up, discovers, again and again and again, the most wonderfully brilliant designs - and these designs have a rationale. We can make sense of them. We can reverse-engineer them, and understand why they are the wonderful designs they are.

Dennett's confidence that, despite all appearances to the contrary, living things are not really intelligently designed rests upon his confidence that there is no intelligent designer. In philosophy this sort of thinking is called begging the question, or less technically, putting the cart before the horse.

Exactly right. If one is determined to believe that an intelligent designer could not exist then what is the point of looking at the other side's arguments and cited data. It is the personally bothersome secondary implications of an intelligent inference that leads opponents of intelligent design to rule it out a priori.

Tuesday, July 11, 2006

Testing Selection Models: Part Two

Wedge with iDesign@UCI has posted a message entilted 'On Evolutionary Explanations.' I've included the last two paragraphs for the purpose of adding commentary. This is the second of two posts on this subject. Wedge's remarks are italicized. Mine are in standard form.

I'm not convinced. You see, I'm a computer scientist. I'm used to looking at incredibly complex, interdependent systems at a high level of abstraction and implementing modifications at the very lowest level. There is very rarely a correlation, even in the most well-designed systems, between what changes appear straightforward at a high level of abstraction and what changes are actually straightforward to implement (by "straightforward" I mean changes which do not require a large number of compensatory changes to other parts of the system). There is not enough detail in the above model (or in most evolutionary models) to evaluate whether or not natural selection is sufficiently powerful to get the job done.

Agreed. The only means of evaluating natural selection's role is through the type of testing used to determine the viability of scientific hypotheses.

This raises an interesting question: How specific does a model have to be to be convincing? That is, how small do the proposed changes have to be to render it likely that natural selection could have filled in the gaps? I don't know of any formal answer to this, but whatever the answer might be it must be able to test natural selection, not merely assert its ability to move between hypothetical intermediate forms described at a high level of abstraction. Ironically, the only people who seem to be interested in doing this sort of thing are design theorists.

That might be because Darwinists have everything to lose and little to gain by testing natural selection. They have succeeded in establishing a role for it based on logical arguments. It is the cornerstone of evolution. Show that the hypothetical intermediate forms do not result from a selection process and you have cut the heart out of Darwinian theory.

Monday, July 10, 2006

Testing Selection Models: Part One

Wedge with iDesign@UCI has posted a message entilted 'On Evolutionary Explanations.' I've included the last three paragraphs for the purpose of adding commentary. Wedge's remarks are italicized. Mine are in standard form.

Take this model of the evolutionary origin of the bacterial flagellum. It is long, detailed, and testable. But just what aspects of the model are testable? Precisely the aspects related to homology. The testable claims are about which components may be more ancient that others, which structures may have been intermediate between the Type-III secretory system and the bacterial flagellum, etc. The question of whether natural selection acting on random variation is powerful enough to make the hypothetical transitions is never addressed. Instead it is assumed that proposing intermediates and telling a story about how each might provide an incremental fitness benefit is enough.

The referenced article attempts to identify homologous proteins, suggest mutations that would enable cooption and identify the basis for selection. Testing of protein structures is of course possible. Identification of different types of mutations is also not difficult. The last endeavor makes or breaks the plausibility of the model. The identification of homologous proteins is consistent with the notion that proteins, believed to have evolved, had precursor functions. Contemplated mutations could be viewed as those that, for example, would produce new binding sites. Such binding sites would enable protein interaction which at first might not be optimal but which would gradually become more efficient through selected mutations.

A pattern is in evidence at this point which will be observed repeatedly. Genes encoding proteins with a specified function undergo mutations leading to the encoding of modified proteins that acquire new functions. This is a thought pattern. It is important to grasp the implications of this before proceeding further. The concept that mutations of existing genes lead to new protein roles, through a gradual modification process conferring increasing functional utility, is a logical argument. It must yield to testable hypotheses before the argument acquires the needed empirical basis. The type of testing required to document the theorized role of natural selection in a cooption process is not satisfied by suggestions from the article.

The author suggests evaluating the role of natural selection through studies of analogies and mathematical modeling. The difficulty with analogies is they tend to be predicated on the same homology circumstances as the model in question. An assumption of their plausibility is built into the assessment process. Mathematical models can be helpful but their reliability is input dependent. The data provided must encompass all relevant variables. A missing one can signify an erroneous outcome. In the end there is no substitution for submitting a biological system to testing.

The type of tests needed are those that show the predicted outcomes. An evolutionary theoretical pathway to irreducibly complex systems argues the viabilty of a model showing gradual adaptative improvements such as was indicated by the binding site description. There should be stages along a pathway to the flagellum structure identified with specific intermediate functions and the protein complexes that enable them. There is a need for tests that demonstrate functional intermediates with biological utility consistent with an incremental build up model. No small amount of bio-engineering is required but the effort is hardly superfluous. Natural selection has been a logical construct since introduced by Darwin. It needs to be placed on a sound empirical footing if concepts like precursor systems and gradualism are to be taken seriously. It is one thing to contend that small incremental changes result in new functions through selective intermediates. It is another matter to demonstrate this experimentally.

A more difficult test would entail simulating an actual mutation process. Mutation rates and mutation types yield to statistical analysis but this looks challenging given long time frames. Nevertheless as the article states: "Science is advanced by proposing and testing hypotheses, not by declaring questions unsolvable." Scientific advances are linked to the production and utilization of biotechnology as well.

The author concludes that proposing an incremental Darwinian model, he calls plausible and testable, undercuts the idea that "extraordinary explanations" i.e. an intelligent inference is plausible. The plausibility of the model is outcome dependent. The outcome of what tests though? Tests of the capacity of natural selection to generate systems through cooption. Anything less makes an end run around Behe's real point; the empirical sufficiency of Darwinian models.

Saturday, July 08, 2006

A Genesis of Darwinian Fundamentalism

References are marked by italics while my remarks are in standard form. The first four paragraphs from an article appearing at ID The Future provide commentary about the relevancy of rationalism to those supporting standard versions of theories attempting to explain the origin and diversity of life. My comments are added.

'Why Evolutionists Can't be Neutral'
Cornelius Hunter

"Rene Descartes hated doubt and wanted to know what he knew with certainty. Descartes wanted to find a method for proving universal truths, and he had just the thing: geometry. Centuries before the ancient geometers had constructed elegant proofs based on a few fundamental axioms. They had discovered a method—logical reasoning based on few rock solid premises—that produced new truths.

For Descartes, one of the great rationalist thinkers of modern times, method was crucial. Euclidean geometry was the template that Descartes would use. Begin with some simple axioms that everyone could agree were true, and then reason your way to new truths. After Descartes, the Cartesians continued to refine and apply rationalism in philosophy and science.

Rationalist approaches hinge on their axioms. Bad axioms lead to bad conclusions, so rationalists need to caveat their conclusions. Instead of claiming a conclusion to be true, they need to make it clear that the conclusion is true if the axiom it relies on is true."

True, but a little too idealistic. Axioms tend to blind those holding them as to the contingency nature of inferences drawn from them. They have a tendency to become articles of faith rather than assumptions open to question.

"In practice, however, things are not so simple. Once rationalism gets rolling it takes on a life of its own. The axioms are taken for granted and assumed to be universal; the conclusions are taken as new truths, method is crucial, and anyone who disagrees must be naïve or nefarious."

Confusing axioms with universal truths leads to Darwinian fundamentalism which frequently surfaces in unmoderated discussion forums. Here is an example.

"A message posted on the Kansas Citizens for Science website by Liz Craig, an officer and public relations contact for the group, outlines the strategy opponents used in 1999 and in the most recent debate.

My strategy at this point is the same as it was in 1999: notify the national and local media about what's going on and portray [advocates] in the harshest light possible, as political opportunists, evangelical activists, ignoramuses, breakers of rules, unprincipled bullies, etc."

Sounds like a true believer who in the name of a cause can justify manipulating the media through funneling a deliberate stream of ad hominem hate words, which if directed at ethnic or sexually oriented targets, would result in censure at best and legal repercussions at worst.