Friday, June 30, 2006

Evidence of Intelligent Design

References are marked by italics while my remarks are in standard form. In a July 6, 2006 entry Joe G. makes the following comments in his blog entitled 'Intelligent Reasoning.'

"Intelligent design begins with a seemingly innocuous question: Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? Wm. Dembski

Yes, they can.

Most, if not all, anti-IDists always try to force any theory of intelligent design to say something about the designer and the process involved BEFORE it can be considered as scientific. This is strange because in every use-able form of design detection in which there isn’t any direct observation or designer input, it works the other way, i.e. first we determine design (or not) and then we determine the process and/ or designer. IOW any and all of our knowledge about the process and/ or designer comes from first detecting and then understanding the design."

Why would advanced intelligence not have detectable properties not dependent on a capacity to describe the exact nature of the intelligent source? Similar entities give rise to similar properties that can be inferred through inductive reasoning and then recognized deductively. 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?

One can argue then that a distinguishing characteristic of intelligent causality is that intelligent cause x would not occur solely as a result of natural forces. If this is a general axiom then ruling out natural forces as an exclusive causal agent would of necessity implicate intelligence as a causal factor. Is it possible to rule out unguided natural forces or at least show that they are very unlikely to produce effect x? If chemical reactions generated a self-replicating structure the reasons why this would or would not be possible should be capable of evaluation. We know the biochemical make-up of cellular components. While defenders of origin of life theories allege that present day cells would not always have existed in their present form we do know what that the end of a chain of events led to. This puts constraints on speculations and requires an end result that is known and measurable.

The biggest source of opposition to intelligent inferences is grounded in different assumptions brought to the table by the different sides. A post from a Yahoo group bearing the name of this blog brings out the point. Comments are directed at a portion of an article cited in a separate post. A comment of interest is the following:

Read mystical event as intelligent causality
albeit a word choice that has distinctly negative
connotations. Waldrop would seemingly ascribe to the
notion that intelligence is an "emergent property" of
matter. Therefore intelligence can be ruled out as a
causal factor unless an intelligent organism
responsible for evidence of it has already been
identified. This in turn leads to two other premises.
First, all physical events must have as their genesis
natural causes devoid of intelligent input. Second,
there can be no possibility of evidence for the
insufficiency of purely physical causes for the
generation of life. One need not confuse the second
premise with detection of the supernatural.
Intelligence is a detectable phenomenon but would be
ruled out of empirical consideration by the noted
philosophical approaches.

The causal factor in this case is connected to the origin of life and it is the sufficiency of events alleged to have given rise to life that are the object of evaluation. Critics of intelligent design oppose the notion that chemical reactions in a prebiotic environment could be seen as an implausible source for the origin of life. They view chemical causality (without intelligent guidance) as the only option. For them an attribution of intelligence as a cause must implicate an identifiable intelligent source. Chemical causality without specification of a pathway is acceptable but an intelligent inference without specifying the identity of the source is not.

Acceptable standards of evidence become an issue. How specific must our explanatory information be? Are inferences possible based on indirect evidence? Based on some well known conclusions this seems to be the case. Dark matter is believed to exist. It is not detected directly. The exact nature of the dark matter is unclear. However postulating its existence allows theorists to plug in a missing parameter, namely the existence of enough matter to explain motions of astronomical objects and theorized small fluctuations in the cosmic microwave background.

Have we observed the evolution of species and the specific genomes that characterize their uniqueness? Are evolution and evolutionary relationships nonetheless inferred based on the indirect evidence of comparative genomic sequences? The acceptability of indirect evidence is not disputed. But arbitrary standards that exclude it from consideration when the indirect inference is intelligence is contrary to a reasonable search for causality. More from the same Yahoo group post:

No consideration is given to the possibility
that chemical reactions are insufficient to cause the
resulting organization which incidently is the product
of encoded nucleic acids. That is why chemical
reactions leading to nucleic acids and proteins get
nowhere without a mechanism that generates a code.
This code however must be generated in the absence of

Opening up indirect inferences of intelligence enables us to reject pure chemical causality when the evidence for such is lacking and the theoretical framework supporting it inadaquate. But what would be positive indicators of intelligence? In other words what are properties of intelligence that enable its identification?

Another post from the group 'Intelligently Sequenced' contains this helpful defining information obtained from the cited internet site.

"Genome: The genome is the message written in DNA. The genome is
information, which is non-material, but measurable, while DNA is a
material substance. Thus, "genome" and "DNA" are not synonyms, nor
are they synonymous with the term "genetic code." The units in
which information is measured are bits and bytes, which are
familiar terms to computer users.

Genetic code: The genetic code is the non-material map of which
letter from the 64-letter alphabet in DNA specifies (i.e., puts in
place in a sequence) which letter from the 64-letter alphabet in
RNA and then which letter from RNA specifies one of 20 amino acids
in the formation of a protein. Amino acids are the 20-letter
alphabet of proteins. DNA, RNA and protein are sequences.

Complexity and orderliness: In information theory, "complexity"
refers to the amount of information required to describe a
sequence. "Orderliness" and "complexity" have opposite meanings.
The more a sequence is orderly, the less it can be complex because
it can be described with a short sequence. The more a sequence is
complex, the less it is orderly because it requires a longer
sequence to describe."

Some important points are worth emphasizing. There is an appropriate distinction made between non-material information and the nucleic acid material that carries the information. In addition there is clarification as to the difference between complexity and orderliness which are often confused. Rather than being equivalent, the two indicate opposing phenomenon. Order, that is predetermined by natural forces, precludes the sequential flexibility that characterizes complexity.

An excerpt from 'Biology: Discovering Life' by Kenneth Miller and Joseph Levine helps focus on the bone of contention:

"Darwin knew that accepting his theory required believing in philosophical materialism, the conviction that matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products. Darwinian evolution was not only purposeless but also heartless - a process in which the rigors of nature ruthlessly eliminate the unfit."

Before further analysing this let's look again at some points made at the Yockey website.

1. The engine of evolution is the genome, which is the non-material information programmed in DNA.

2. Introducing a requirement for an Intelligent Designer is ad hoc and invalid. Explanations of the requirement for an Intelligent Designer almost invariably are “inferred” from non-living matter, usually a machine of some kind. Machines require an “Intelligent Designer” to exist—or evolve—because they do not have a genome. Living things do not require an ad hoc “Intelligent Designer” to live and evolve because they DO have a genome.

The crux of Intelligent Design “theory” is therefore to maintain that the Intelligent Designer substitutes for the genome in evolution. However, the genome evolves through a random walk and has no need of an Intelligent Designer.

Having done an excellent job at defining terms the author goes astray in erroneously concluding that an intelligent design inference is an evolutionary substitute. One can make that argument although it is not the argument or focus of this post. Before evolution "through a random walk" can occur a genome must exist. The intelligent design inference is origins based. As Miller and Levine correctly pointed out Darwinism is philosophically conjoined to materialism. Yockey's point about the non-material nature of the genome is right on target. If "matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products" then Darwinists have already lost the war on a battlefield strewn with corpses labeled chemical necessity and natural selection. Chemical necessity determines order not complexity. Change upon which natural selection is said to act presupposes a flow of information made possible by a non-material genome's existence. The information conveyed by Kenneth Miller, Dr. Hubert P. Yockey and the author of this post has an intellectual genesis. The medium may be electronic or ink but the information carrier is a follow-up construct. Intelligent design has correctly identified the significance of sequential order and its implication for life's origins.

Genetic Transcription Pauses- Discarding randomness

A Stanford University news report offers insight as to why RNA polymerase pauses during the transcription process. Some general information from the first two paragraphs of the article:

"Of the thousands of proteins produced in our cells, few are as important as the enzyme RNA polymerase (RNAP), which has the unique ability to faithfully copy genetic information from DNA. In fact, all organisms—from bacteria to people—depend on RNAP to initiate the complex process of protein synthesis. Despite its crucial role in cell biology, fundamental questions remain about how the RNAP enzyme actually works.

Now scientists from Stanford University and the University of Wisconsin-Madison have solved part of the puzzle. Writing in the June 16 edition of the journal Cell, the research team found that a molecule of RNAP makes frequent pauses at specific sites along the DNA double helix. This finding comes on the heels of the team's 2003 discovery that RNAP enzymes routinely make thousands of brief stops ("ubiquitous pauses") when carrying out the vital task of transcribing genetic information from DNA to RNA—a process called transcription."

[Bradford]: The author gets to the meat of the matter later in the article.

"That's great," Block said. "It's telling us that the enzyme is doing just what it should. After all, it's seen the same sequence eight times in a row, so it had better do the same thing eight times in a row. It also paused at several other sites as well, which is interesting. Sometimes it paused longer, sometimes shorter, but the average was remarkably the same—about a second or so. We also discovered that it just didn't stop at any old sequence but at very specific places where there's a signal in the DNA that basically says, 'Pause here.'"

That signal, he added, occurred for specific sequences in the DNA. "We found that there is always a G near a specific pause position, and always a T or a C at another nearby position," he said. "So the pause seems to be sequence dependent. It's not always the same duration every time, but it's more likely to pause at one of these sites than at any other sites in between, so it's not just some random phenomenon that happens every once in a while. If I'm running down the road and I trip, that would be a random phenomenon. But if I run down the road and every time I trip there's a pothole, then that's not random."

Some researchers have argued that all pauses might be associated with either hairpin formation or backtracking, but the Cell study contradicts that assumption. "Most ubiquitous pauses have nothing whatsoever to do with backtracking or hairpins," Block said. "We think ubiquitous pauses are the most common and probably most important kind of pause, and the models that some biochemists have been using are just wrong."

[Bradford]: So pauses seem to be sequence dependent and not random. Removal of randomness as a causal agent when knowledge of actual causation comes to light is a familiar theme. More knowledge of genomic dynamics should dispel other ideas grounded in ignorance like the belief that unknown function equates to "junk DNA."

Thursday, June 29, 2006

Debunking Arguments for Life's Origins

Comments on an article accessed at the referenced URL involved the possibility of an exchange between an individual identified as Timothy Chase and me. Unfortunately the opportunity to post a response was closed off before I could respond (it seems to occur frequently) so I'll post a blog response. The authors and the referenced paper are identified for clarity. The URL brings one to an article entitled 'Scientific world unites over origins of life' which was authored by Eben Harrell. Comments follow the article.

Timothy Chase wrote:
It is grounded in a fair amount of circumstantial evidence -- and to some extent, a general understanding of the scientific method. For example, the boundary between life and non-life has borderline cases. Viruses are a good example. We know, for example, that an enzyme and nutrients are all that are required to form a self-replicating RNA virus. (See #41 above -- which includes technical references and links to the original articles.)

[Bradford]: You neglected to point out that a "self-replicating" RNA virus is dependent on transcription mechanisms of its host for replication. The host transcription function is highly complex and as necessary to successful replication as the viral nucleotide sequence. As stated in the article that you referenced "New viroids and virusoids are synthesized by the host cell as long precursors in which the viroid structure is tandemly repeated."

Chase: Likewise, we know that natural processes form amino acids under circumstances which evidently existed on the early earth with its reductive atmosphere -- prior to the continual production of corrosive oxygen through photosynthesis. Likewise, we know that stable ribose can be formed under natural conditions.

[Bradford]: Spark discharge experiments producing amino acids show why functional proteins would not form as a result of lightning storms. Experiments show that amino acids are found in a larger mixture containing other biochemically useless organic compounds. The amino acid mixtures are of equal amounts of left- and right-handed stereoisomers and sets of 20 varieties are not produced. Lacking are experimental reasons to believe that an extracellular chemical process exists leading to the separation of L amino acids from the much larger organic mix. Most importantly there is no empirical basis for believing amino acids would form polymers leading to functional proteins. Functionality is sequence dependent.

Formation of ribose, like other biomolecules, may be found to occur naturally under limted conditions. But this does not address the primary issue confronting OOL advocates. Nucleic acids, useful to living cells, are distinguished by the specificity of their nucleotide sequences. It is the identity and order of codons that confers selective value. Chemistry can explain why ribose might be part of reaction x that leads to bonds with nitrogenous bases and phosphate groups but this does nothing to explain why particular sequences useful to protein synthesis and replication functions would arise. Also lacking is a means of genetic expression. OOLers typically issue promissory notes at this juncture indicating their faith in future expermental results. However this ignores a problem that goes deeper than results. Natural selection, a crtical component of Darwinian models, is powerless to provide any predictive insight as to why we should expect a narrow subset of sequence specificity within a much broader range of possibilities when a cell whose existence is dependent on that specificity has yet to evolve. This defect pierces the heart of Darwinian theory.

Chase: As #41 demonstrates, self-replication doesn't require a cell per se -- and doesn't even require a genome to arrive at a self-replicating genome. Likewise, a metabolism is essentially an autocatalytic chemical reaction and wouldn't necessarily require any genome at all, or for that matter, an enzyme. Likewise, a cell is essentially a semi-permeable compartment, and some geological formations could act as a primitive "cell" of sorts. There are of course other problems, smaller missing pieces. More importantly, putting all of the pieces together into a coherent theory which fits the evidence we have so far as to what conditions existed on the primitive earth, and which is capable of making specific, testable predictions.

[Bradford]: Let's take a look at one of the papers indicated by a URL you provided. From the paper entitled 'An Extracellular Darwinian Experiment with a Self-Duplicating Nucleic Acid Molecule':

"Experiments were performed to explore the evolutionary consequences for a self-duplicating nucleic acid molecule put under selection pressure for fast growth. As the experiment progressed, the rate of RNA synthesis increased and the product became smaller. By the 74th transfer the replicating molecule had eliminated 83 per cent of its original genome, becoming the smallest known self-duplicating entity."

[Bradford]: Two points of note here. The biomolecules relevant to the experiment are sourced from existing biological entities. The RNA in question did not evolve in a prebiotic soup and the replicase noted in the paper (a protein) also was not the product of a prebiotic process. Second, the replication was a downsizing process whose significance will be the subject of further comments.

More from the paper:
"...Further, the sequences involved in the recognition mechanism between template and enzyme are enriched in the smaller molecules which evolve."

[Bradford]: It is expected that RNA would change as it is unstable and for this reason unsuitable as a long term carrier of genetic information; a task handled by DNA.

"Finally, these abbreviated molecules have a very high affinity for the replicase but are no longer able to direct the synthesis of virus particles. This feature opens up a novel pathway toward a highly specific device for interfering with viral replication."

[Bradford]: Loss of a function does not support an assumption that RNA would then acquire a new distinct function. The affinity for replicase results from some very specific amino acid sequences in the enzyme active site as well as the secondary structure of the enzyme to say nothing of its very existence which is a given to begin with. Evolution of a functional genome on prebiotic earth would require the evolution of larger not smaller molecules.

The last sentence is interesting in that it points to some state of the art application of truncated RNA. RNAi has already shown promise as an anti-viral agent. On that point we can agree.

Wednesday, June 28, 2006

Algorithmic Perspectives

One of my favorite blogs is iDesign@UCI. The authors are generally thoughtful, original and analytical. It makes for a good mix. A URL leading to a particular post at the blogsite is provided. My comments are included.

Friday, June 23, 2006
Compositional Evolution
I'm reading through a new book, Compositional Evolution by Richard Watson, and it is really interesting. Watson's thesis is that certain evolutionary methods of variation (sexual recombination, lateral gene transfer, symbiotic encapsulation, etc.) are fundamentally distinct in an algorithmic sense from the traditional gradualist framework (in which beneficial mutations are accumulated in a linear fashion). Gradualism operates as a hill-climbing search strategy, and is therefore prone to get stuck in local optima. Compositional mechanisms, on the other hand, are apparently able to escape them (in systems with a semi-modular relationship among their variables) by combining pre-adapted genetic data from two distinct lineages.

Watson is a computer scientist, and examines evolution from an algorithmic perspective. The admission and proof of the inability of gradualism to evolve systems with strong dependencies among its variables is refreshingly frank. He presents a substitute mechanism, of course, so the book is not supportive of ID. Still, it helps formalize and highlight the issues involved, in a way that makes them easier to talk about. Computational Evolution is definitely worth a read if you're interested in looking at evolution from an algorithmic perspective – especially if you'd like to critically evaluate the power of evolutionary search strategies.
Posted by Wedge at 8:18 AM

William Bradford said...
Watson may change the focus by centering it on compositional mechanisms but such mechanisms do not address objections to standard models. Modular models merely move problems with gradualism down a logical chain. Gradualism is inherent to any life origins paradigm absent any assumptions that encoded nucleic acids and functionally sequenced proteins came prepackaged with the begining of the universe. The difficulty for Watson and others is they cannot avoid a gradualist approach to a minimal genome and functional cell. They must assume an intricate level of interacting biological modules before any algorithm becomes plausible. When Watson nails down a module applicable to basic protein synthesis and metabolic functions he will have something worthwhile.
6/26/2006 5:36 PM

Wedge said...
This is absolutely true. I think Watson's results are algorithmically interesting but they don't explain, as you point out, how the compositional operators which he analyzes might have arisen.

[Bradford]: Therein lies the problem for those wanting to exclude an intelligent inference. It is strongest at the point of life's origin where abiogenesis is embarrassingly inadaquate from a naturalist perspective.

Monday, June 26, 2006

Teaching Evolution

This article, at the referenced URL, is the basis for the identified comments that follow.

'Scientific world unites over origins of life'

"THE world's leading scientists have issued a damning statement against the teaching of creationism in schools, arguing that denying the facts of evolution damages the development of children.

The national science academies of 67 countries, including the Royal Society, issued a joint statement warning that scientific evidence about the origins of life was being "concealed, denied, or confused" in many schools."

[Bradford]: This comment surprised me. I would expect a complaint about confusion related to the evolution of organisms not "scientific evidence about the origins of life." What "scientific evidence" did they have in mind? Scientific evidence indicates that prevailing theories of abiogenesis are theoretically flawed and lacking in empirical evidence.

"It added that teaching children about Darwinian evolution and the natural world was integral to protecting the planet."

[Bradford]: Protecting the planet? This is rambled thinking gone into overdrive.

"The statement aims to present a united front against the teaching of creationism and intelligent design in schools in the United States, the UK and elsewhere.

Creationism argues that the origin of life on earth is recent and divine and that all forms of life have always existed in their present form.

Intelligent design, which has been called "thinly veiled" creationism, argues that some species are too complex to have evolved through natural selection and must therefore be the product of a "designer".

The statement says: " Knowledge of the natural world in which they live empowers people to meet human needs and protect the planet. [Life has] evolved in ways which paleontology and the modern biological sciences are describing and confirming with increasing precision."

It continues: "Within science courses taught in certain public systems of education, scientific evidence ... [is] being concealed, denied or confused with theories not testable by science."

[Bradford]: Or not falsifiable as is the case with standard origin of life hypotheses right? The truth is that what is being concealed is evidence against abiogenesis and evolution. Why not place greater emphasis on the lack of evidence for the generation of basic and universal systems like the transcription and translation functions related to protein synthesis or universal metabolic pathways? There are legitimate complaints that can be made about the teaching of scientific evidence related to the origin and diversity of life. Teaching should encourage critical thinking by encompassing biological systems that are problematic for standard theories. Otherwise we risk confusing good teaching with indoctrination.

Christianity, Science and the Promotion of Mythology

In a commentary by Chuck Colson dated 6/26/06 and entitled 'Hidebound Nonsense'
Colson discusses a historic myth that passess for sophistication among Darwinian diehards. How would you describe the Middle Ages? A time of intellectual stagnation? If so some remedial history is in order. Medieval mythologies persist to this day thanks to their capacity to promote ideology rather than truth. Colson attempts to correct the record with the following essay which can be accessed at the noted URL.

"Earlier this year, Britain’s Channel Four aired a two-part special entitled “The Root of All Evil.” No, it wasn’t about money, greed or materialism. Nor was it about racism and other forms of hatred. The “root” was religion, specifically Christianity.

The special featured Oxford professor Richard Dawkins, arguably the most famous apologist for the Darwinian worldview. While Dawkins may be an expert on Darwin, it’s clear that he knows little about history, especially the history of Christianity.

Besides the old saw that religion causes violence—as opposed to peaceful atheism, as practiced by Stalin and Mao—Darwinists charge Christianity with promoting superstition and ignorance. Dawkins calls faith a “process of non-thinking” where the “hidebound certainty” of believers stifles human curiosity. According to Dawkins, for science to take off at all, humanity had to escape the “little” and “pokey” view of the cosmos it inherited from medieval Christianity.

The only “hidebound certainty” here is the nonsense that Dawkins is spouting. The truth about Christianity and science is, in fact, exactly the opposite.

As Rodney Stark tells us in his recent outstanding book, The Victory of Reason, when Europeans first began to explore the rest of the world what surprised the most wasn’t what they saw—it was “the extent of their own technological superiority.”

What made the difference? Why was it that while “many civilizations,” such as the Chinese, had pursued alchemy, but only in Europe did it lead to chemistry?

According to Stark, the answer ultimately lies in European Christianity. While other religions emphasized “mystery and intuition,” Christianity “embraced reason and logic as the primary guides to religious truth.” From the start, the Church Fathers “taught that reason was the supreme gift of God and the means to progressively increase understanding of Scripture and revelation.”

This regard for reason wasn’t limited to theology. St. Augustine wrote of the “wonderful—one might say stupefying—advances human industry has made.” He attributed these to the “unspeakable boon” to our “rational nature.”

This view of reason gave rise to the medieval universities of whose existence, or at least origins, Dawkins seems to be totally ignorant. As Stark puts it, “faith in the power of reason infused Western culture” in a way it did no other society. It prompted “the pursuit of science and the evolution of democratic theory and practice.”

The very Middle Ages Dawkins belittles saw great scientific and technological advancements that Stark chronicles, including the desire to explore God’s created world—the impulse that gave rise to Christians who were scientists producing what we now know as the scientific method. To say that these were nothing more than the Dark Ages is not only wrong—it’s a lie. Unfortunately, it’s a lie with legs as Britain’s Channel Four demonstrated. That makes the Victory of Reason must reading for any serious Christian. It contains some of the best apologetic arguments I’ve come across yet."

Saturday, June 24, 2006

Christianity and Science- Part Two

An article written by Nancy Pearcey entitled 'Christianity Is a Science-Starter, Not a Science-Stopper' can be accessed at the referenced website. This is the second post devoted to the article. The prior post can be accessed at:

From the referenced URL:

'Polytheistic Religions'
'Other religions typically differ from Christianity on one of two major points. The God of the Old and New Testaments is a personal being, on one hand, while also being infinite or transcendent. Many religions throughout history have centered on gods who are personal but finite--limited, local deities, such as the Greek or Norse gods. Why didn't polytheistic religions produce modern science?

The answer is that finite gods do not create the universe. Indeed, the universe creates them. They are generally said to arise out of some pre-existing, primordial "stuff." For example, in the genealogy of the gods of Greece, the fundamental forces such as Chaos gave rise to Gaia, the great mother, who created and then mated with the heavens (Ouranos) and the sea (Pontos) to give birth to the gods. Hence, in a polytheistic worldview, the universe itself is not the creation of a rational Mind, and is therefore not thought to have a rational order. The universe has some kind of order, of course, but one that is inscrutable to the human mind. And if you do not expect to find rational laws, you will not even look for them, and science will not get off the ground.

This insight into polytheism goes back to Isaac Newton, who once argued that the basis for believing there can be universal laws of nature is monotheism, since it implies that all of nature reflects the creative activity of a single Mind. Newton was arguing against the Greek notion, still prevalent in his day, that the earth was a place of change and corruption, whereas the heavily bodies were perfect and incorruptible. Against that view, Newton believed that both were products of a single divine Mind and therefore both were subject to the same laws. This opened the way for his breakthrough concept of gravity--the then-revolutionary idea that the same force that explains why apples fall to the ground also explains the orbits of the planets.[9]

More recently a similar argument was made by the Nobel Prize-winning biochemist Melvin Calvin. Speaking about the conviction that the universe has a rational order, he says, "As I try to discern the origin of that conviction, I seem to find it in a basic notion . . . enunciated first in the Western world by the ancient Hebrews: namely, that the universe is governed by a single God, and is not the product of the whims of many gods, each governing his own province according to his own laws. This monotheistic view seems to be the historical foundation for modern science."[10]'

[Bradford]: A key characteristic of Judeo-Christian beliefs- monotheism- generated a fertile climate for the birth of science. The testimony of a scientific giant, Isaac Newton, is evidence for the impact of monotheism on his considerable contributions. Melvin Calvin's comments are icing on the cake.

Sunday, June 18, 2006

The Last Word

The exchanges involving Aleph Wilton, John Rennie and me have come to an end with a decision by Rennie to terminate further comments. He gets the last word in the forum he controls. Further comments by me are addressed to Rennie's last post to which Aleph was unable to reply. As always my comments are clearly delineated from the initial post. In addition, for the sake of clarity, parentheses are used to indicate names and information apart from the original text.

Comment from: John Rennie [Member]
Sorry, you're right, you didn't ask the following as a question. It was just a flatly misleading remark.

(Aleph): Darwinism, despite its 150-year headstart, has yet to "tell" us anything, one single thing, about the origin of life....

(Rennie): Hence my reply.

(Rennie): Evolution hasn't produced a lot of answers about the origin of life because (do I hear an echo?) evolutionary theory isn't primarily about the origin of life.

[Bradford]: But debunking ID (which Rennie spends much time attempting to do) necessarily entails the issue of abiogenesis.

(Rennie): You keep trying to use unsolved mysteries about the origin of life as a club to beat up evolution, and I keep pointing out that this is like criticizing a BMW for being an awkward paperweight.

[Bradford]: They are unsolved mysteries only in the minds of dedicated Darwinists like Rennie. Scientific evidence, about which we presume Mr. Rennie has some concern, indicates that living cells come only from other cells. Criticizing abiogenesis on scientific grounds is legitimate and laudable. Why equate questions about the validity of an origin of life hypothesis with questioning evolution.

(Aleph): For one thing, the theory of evolution is hardly the central principle of contemporary biology. That description must surely be reserved for the thesis that all of life is to be understood in terms of the "coordinative interaction of large and small molecules" (James Watson, The Molecular Biology of the Gene).

"[Evolution] is a general postulate to which all theories, all hypotheses, all systems must hence forward bow and which they must satisfy in order to be thinkable and true." (The first part of Dobzhansky's quote continued below)

[Bradford]: Bowing before postulates is an updated version of idolotry.

"Evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow — this is what evolution is." From the essay Nothing in Biology Makes Sense Except in the Light of Evolution, by the pioneering geneticist and evolutionary biologist Theodosius Dobzhansky (1973).

[Bradford]: The trouble is evolution does not illuminate key issues. The evolution of prokaryotes to eukaryotes is argued largely based on endosymbiosis, which even if assumed, does nothing to explain notable phenotypic differences unrelated to organelles. These differences lack a theoretical explanation much less one supported by empirical evidence. A mutation mechanism is fraught with difficulties and natural selection is primarily a logically argued concept rather than one sustained by experimental data.

(Rennie): Dueling quotes aside, doesn't it strike you that this "central principle of contemporary biology" is a tad broad as it stands, and would include much of chemistry? And do you really want to imply that Jim Watson doesn't think evolution is central to biology? The same James Watson who wrote (in "Why Darwin is Still a Scientific Hotshot," in the Los Angeles Times):

[Bradford]: Biology does include chemistry. Why not then depict enzymes, described as conserved, by a term referring to the chemical affinity between active sites and substrates as this would convey more useful information and be more precise than an evolutionary hypothesis? Watson is of course a proponent of evolution but he is accurate in pointing out the importance of understanding the "coordinative interaction of large and small molecules." Such an understanding has immediate scientific applicability. Suppositions about natural history do not.

(Rennie): Let us not beat about the bush — the common assumption that evolution through natural selection is a "theory" in the same way as string theory is a theory is wrong. Evolution is a law (with several components) that is as well substantiated as any other natural law, whether the law of gravity, the laws of motion or Avogadro's law. Evolution is a fact, disputed only by those who choose to ignore the evidence, put their common sense on hold and believe instead that unchanging knowledge and wisdom can be reached only by revelation.

[Bradford]: This is scientific lunacy. Laws pertaining to motion, gravity and chemistry are mathematically definable indicating a precision that has been repeatedly verified experimentally. Evolution is not a law. You do not get useful predictive results from applying evolutionary principles. What you do get are general statements accompanied by frequent adjustments for results not conforming to expectations. You get extrapolations that greatly exceed what evidence points to and much speculation about events in natural history for which evidence is either unavailable or has been erased with time.

(Rennie):In answer to my request for an experiment for testing I.D., you wrote:

(Aleph): Have ID proponents claimed that they can "test between two extremely different conceptions of how a designing intelligence created life?" Why should ID's leading proponents propose such a scientific test? Because you bang your spoon on your high-chair tray?

Rennie: No, don't do it for my sake. Do it because it's one of the minimal requirements that an idea should meet to qualify as a scientific theory.

And so on. You say I'm mischaracterizing your remarks, but from here it seems like you're just reluctant to explore what your ideas actually mean (or fail to mean).

[Bradford]: You can apply a test that is applicable to both the concept of selective changes and ID. Knock out a gene required for the function of a critical system. There are many posibilites. Try one related to a growth factor required for cellular replication. Place organisms so afflicted in a suitable environment and observe the evolution or non-evolution of the required function. This general approach should yield results one way or another.

(Rennie): You keep reiterating your dismissal of the criticism of Nelson's remarks, but you won't actually say where or how that criticism is factually baseless.

Anyway, enough of all this. If life in New York teaches us anything, it's that if you spend all your time yelling back at the crazy people who scream on streetcorners, then you have become one of those crazy people. And I do have more constructive things to do with my time then continue this.

[Bradford]: Anyone who disagrees with you must be crazy right John?

So with that in mind, it's time to bring the ridiculous exchanges in this comment thread to an end. Aleph, it's clear that you've already made whatever point you're willing and able to make. Intelligent readers should have a pretty good idea of who is representing a reasonable scientific argument and who is not.
June 18, 2006 @ 12:49

[Bradford]: I've read a series of posts by Rennie in this thread that have a common theme. There is much claimed both for standard theories and in opposition to ID and little scientific data offered in support of the claims. Don't restrict yourself to this one post. Take in a few of them at this address:

Saturday, June 17, 2006

Christianity and Science- Part One

An article written by Nancy Pearcey entitled 'Christianity Is a Science-Starter, Not a Science-Stopper' can be accessed at the referenced website. A part of it is quoted with my identified comments included.

"The default position for many Americans in the Blue States seems to be that Christianity is a "science stopper"--that religion implies a world of perpetual miracle, closing off the search for natural causes.[3] This is often coupled with the familiar cliché that over the centuries the Christian church has intimidated, silenced, and persecuted scientists. A few months ago, a journalist repeated the shop-worn stereotype, writing that "proponents of Copernicus' theory were denounced as heretics and burned at the stake."[4] A columnist recently wrote that Copernicus "scandalized the world--and more important, the Catholic Church--with his theory of heliocentric cosmology." The same pattern continues today, the columnist goes on: "The conflict of religion and science sounds all too familiar. Darwin still has trouble getting past creationist gatekeepers in some school districts."[5] The story of conflict does sound familiar, because it is the standard interpretation of history taught all through the public education system. In fact, it is so widely accepted that often it is treated not as an interpretation at all, but simply as a fact of history. Yet, surprising as it may sound, among historians of science, the standard view has been soundly debunked. Most historians today agree that the main impact Christianity had on the origin and development of modern science was positive. Far from being a science stopper, it is a science starter."

[Bradford]: Pearcey is attempting to substitute historic facts where distortion and untruth currently hold sway. As she has done in the past Pearcey is identifying and debunking a pernicious myth that portrays Christianity as a hindrance to scientific progress.

"One reason this dramatic turn-around has not yet filtered down to the public is that the history of science is still quite a young field. Only fifty years ago, it was not even an independent discipline. Over the past few decades, however, it has blossomed dramatically, and in the process, many of the old myths and stereotypes that we grew up with have been toppled. Today the majority view is that Christianity provided many of the crucial motivations and philosophical assumptions necessary for the rise of modern science."[6]

[Bradford]: Fair enough but this does not explain why these myths and stereotypes developed in the first place. Understanding that entails acknowledging a duality of thinking that has pervaded western thinking since the inception of Christianity. Since the apostles first began spreading Christianity in the first century there has existed a large segment of society hostile to its message. The open persecution of the Roman era ceased but opposition to Christianity continued; taking more subtle approaches since then. Anti-Christian elements in the west have succeeded in making their viewpoints predominant and thought of as mainstream thinking. This is evident in inaccurate descriptions of key events in history. Nancy Pearcey accurately documents these events.

"In one sense, this should come as no surprise. After all, modern science arose in one place and one time only: It arose out of medieval Europe, during a period when its intellectual life was thoroughly permeated with a Christian worldview. Other great cultures, such as the Chinese and the Indian, often developed a higher level of technology and engineering. But their expertise tended to consist of practical know-how and rules of thumb. They did not develop what we know as experimental science--testable theories organized into coherent systems. Science in this sense has appeared only once in history. As historian Edward Grant writes, "It is indisputable that modern science emerged in the seventeenth century in Western Europe and nowhere else."[7]

This fact is certainly suggestive, and it has prompted scholars to ask why it is that modern science emerged only out of medieval Europe. Sociologist of religion Rodney Stark identified the 52 figures who made the most significant contributions to the scientific revolution, then researched biographical sources to discover their religious views. He found that among the top contributors to science, surprisingly only two were skeptics (Paracelsus and Edmund Halley).

Stark then subdivided his subjects once again into those who were "conventional" in their religious views (that is, their writings exhibit the conventional religious views of the time), and those who were "devout" (their writings express a strong personal investment). The resulting numbers show that more than 60 percent of those who jumpstarted the scientific revolution were religiously "devout."[8] Clearly, holding a Christian worldview posed no barrier to doing excellent scientific work, and even seems to have provided a positive inspiration."

[Bradford]: But you would never grasp this based on information imparted in our educational institutions from elementary levels on up. Pearcey emphasizes that far from being a hindrance to science, Christian influences led to its pursuit by early scientific pioneers. In addition the fact that science did not evolve in cultures lacking a significant Christian influence is not lost on Pearcey nor should it be on her readers.

What were the key elements in that inspiration? Let's highlight several basic principles by drawing a series of contrasts to other religions and philosophies. If we make the claim that Christianity played a causative role in the rise of modern science, to be scientific about the matter, we must also rule out other possible causes. Since as a matter of historical fact, no other religion or philosophy did play the same causative role, the best way to phrase the question is, Why didn't they?

[Bradford]: Good question and not one likely to be pursued by those who would depict science and Christianity as inherently in conflict.

Friday, June 16, 2006

My Response to John Rennie

Today I posted this response to Rennie's comments directed at what I had previously written. The website address is provided.

Comment from: John Rennie [Member]
William Bradford: When I asked you for a scientific investigation into the origin of life that built on I.D., you replied:

Since the hypothesis indicates that life and critical cellular systems do not arise in the absence of intelligence any experiment testing the capacity of such a system to evolve under conditions involving selective pressure could either substantiate standard theories or provide evidence that the first hypothesis is correct. Knocking out targeted genes of a biological system in question could simulate a point in time prior to their evolution.

The italicized words are what led me to say you were suggesting that selective pressure (obviously imposed by human intelligence in this case) could help to prove the case for I.D. But if I've misunderstood your proposal, let's scratch that and try again. Please restate exactly what experiment(s) you are proposing one could do, and what conclusions we could draw from them that aren't simply reassertions of I.D.'s tenets.

Bradford: Here is a quote of yours that you left out:

"It's nonsense to say that experiments showing that selective pressure could produce life prove your hypothesis--for one thing, you didn't try to disprove the hypothesis."

Bradford: I did not use the term "prove" the hypothesis but rather stated that the experimental outcome would provide evidence that the first hypothesis is correct. These hypotheses are supported or debunked based on a broad range of evidence. If you're looking for proofs look toward mathematics.

See my comments above to Aleph Wilson about the practical necessity of defining in some way the Intelligence behind I.D. and its capabilities if you're to test I.D. hypotheses.

Bradford: What is required is evidence consistent with intelligent causality- the hypothesis. By the way, practical necessities entail falsification criteria. How is abiogenesis falsified?

IDers look at the only actual evidence we have- life itself. Biological systems provide evidence inconsistent with the hypothesis that life arises in an extra-cellular environment. There is no need to make assumptions for we know that a functional, replicating cell is the end result. Investigations as to how chemical reactions produce an encoded genome will continue to be fruitless because the orderly arrangement of codons is not generated by organic chemical reactions unless a precoded nucleic acid template already exists. Encoded conventions are evidence for intelligence.

Thanks for a fine example of I.D. circular logic. You're saying that biological systems are inconsistent with abiogenesis because, well, they just are.

Bradford: No. I'm stating that a biological system whose synthesized end products are part of the synthesis mechanism indicates an insurmountable obstacle to OOL theories. How do 20 tRNA amino acyl synthetases "arise" under prebiotic conditions? Is there a genetic encoding mechanism in place and if so how is it expressed? If not what would be the basis for a selection process and how would selected changes be conserved? Do you even have a coherent theoretical mechanism allowing for a logical explanation as to how events unfolded? Can you explain the sequence of events that led to the generation of universal metabolic pathways? Did they follow or preceed the "arising" of encoded nucleic acids? Can OOLers at least tell us how natural selection would operate in a prebiotic environment?

What you're missing is that abiogenesis researchers are not claiming that whole, complex cells suddenly assemble themselves out of the dust. They're investigating how simple molecules can organize into more complicated systems, and how these in turn might gradually evolve toward structures more and more like living cells.

Bradford: What you're missing is a theoretical framework that provides any guidance as to how a transition process from non-life to a replicating cell proceeds. Simple molecules do not organize themselves into nucleic acids with protein encoding capacities. The encoded nature of nucleic acids is a function of their codon make-up and sequential order as well as a capacity to replicate it. You won't get that from reactions in a prebiotic environment. But you are invited to explain how a gradual process leads to a cell. How does natural selection apply?

Perhaps that quest will fail, and science will never learn how life arose. That's a very real possibility. But I.D. explanations will never be scientific ones until you can present evidence for the existence of the Designing Intelligence that comes from something other than the phenomenon you're trying to explain.

Bradford: Why should future space explorers not infer an intelligent cause if they find engraved life forms on mountains of a newly visited planet even if no intelligent life is found on that planet?

Bradford: If you anti-IDists would be willing to concede that intelligent causality is a reasonable inference about which reasonable people differ it would be good for all.

Now you're making exactly the same silly argument that Nelson did. Scientists have no problem with invoking intelligent causality when the existence of the intelligence in question is already an established fact.

Bradford: Scientists and non-scientists alike would have no trouble inferring an intelligent cause even when the intelligent agent is not identifiable. Intelligence is associated with unique properties. Biology is excluded from the mix a priori by some because secondary implications make them uncomfortable.

When we see the scene of a robbery, we can attribute it the cause to an unseen thief because we know that thieves exist. But it would be crazy to attribute the disappearance of a CD player to, say, invisible robotic termites that eat consumer electronics. Invoking "intelligence" as a causal agent doesn't mean anything unless you're willing to define that intelligence in some embodied way. I.D. is not a spur for further research; it's an excuse to stop asking questions.

Bradford: Nonsense. The questions asked become the important ones. Rather than waste resources on origin of life research we can divert them to asking what is the cause of a health malady and what would remedy the problem. Those kinds of questions will always exist and those asking the questions are not confined to believers in life from unspecifed and unknown prebiotic pathways. The stop asking questions canard is an invented dilemna.

Wednesday, June 14, 2006

An Attempt to Discredit ID

Denyse O'Leary illustrates how eagerness to discredit intelligent design leads to a misrepresentation on the part of someone who should know better. Here is a snippet from her post on which my comments are clearly identified. From the following website:

'Pagans and intelligent design:'

"In one of yesterday's posts, I commented on Vatican astronomer Guy Consolmagno claiming that six-day creationism was a form of "paganism," which is clearly erroneous. It is a form of fundamentalism (literal interpretation of the Bible), which originated with Christianity and other "religions of the Book" and has no pagan roots whatever. Nor could it have such roots."

[Bradford]: One would think a Vatican astronomer would be able to distinguish between biblical and pagan influences. O'Leary is right on target. Six day creation is a belief held by those who hold to a literal or (as they would likely assert) straightforward interpretation of Genesis. The belief clearly results from a reading of scripture rather than a pagan influence.

"The pagans' only book is nature itself (the "book of creation," as it was formerly called). However, once an actual book is accepted as a divine revelation (Torah, Bible, Koran), it can be quoted with authority. But such books only came into existence with monotheistic religions.

The fact that Consolmagno can get away with such misrepresentations shows how eager many in the science community are to hastily shelve the discussion of intelligent design, citing any old nonsense that sounds pleasant to digest."

[Bradford]: Exactly.

"For anyone who wants to know facts in this area, there are actually "pagans" (sometimes called "heathens") in North America. To my knowledge, they are not particularly friendly to creationism (young earth or ancient earth) or to any type of intelligent design. (Scroll down or search on the term "intelligent design.")"

Monday, June 12, 2006

A Genetic Switch

An article published by the Howard Hughes Medical Institute entitled "Genetic Switch for Maturation Discovered," which can be accessed at the indicated web address, provides some food for thought. A snippet from the article appears here. My interspersed comments are clearly identified.

"The genetic maturation switch identified by the researchers, called DHR4 , is a member of a family of genes that encode proteins called nuclear receptors. These receptors, triggered by hormones, each control a large number of other genes, giving them a critical role in coordinating complex body processes."

[Bradford]: It is precisely such genes that should be the focus of attention by evolutionists and advocates of intelligent design. If the existence of eukaryotic organisms results, to a great degree, from a process dependent on selected random mutations then evidence for a capacity to generate novel complexes of genes triggered by hormones is essential. The potential of such gene complexes to evolve offers IDers opportunities to make predictions. As engineers or others who design products are aware, a seemingly simple modification of one part can entail the necessity to modify other interacting parts as well. Any attempt to describe the potential of genetic change required to generate a contemplated morphological feature needs to incorporate an estimate of inhibiting factors represented by existing genomic properties. Quantification is difficult due to an enormous number of variables, incomplete knowledge and an inherent uncertainty pertaining to data associated with natural history. Nevertheless an honest search for truth demands that theory encompass these kinds of details with the outcome not presumed.

"Thummel and his colleagues began studying DHR4 because of its pattern of activity in the developing fly and other insects. “Virtually nothing was known about DHR4 , but we found it intriguing because it is expressed transiently during the very early stage of metamorphosis,‿ he said. DHR4 was also intriguing to the scientists because the gene produces a so-called “orphan‿ nuclear receptor, whose activating hormone was unknown.

To discern the function of DHR4 , the researchers knocked out the gene in two different ways. Co-author Charles created a mutant form of the fly that completely lacked a functioning gene. And Thummel and his colleagues used a technique called RNA interference that allowed them to selectively inactivate the DHR4 gene at different stages of the fly's growth."

[Bradford]: Gene knock out is an effective tool. It has been mentioned as one that might be used in connection with experiments testing the capacity of a biological function to evolve under selective pressure. Rapidly reproducing organisms would be used and the time frames could span years.

"By analyzing the effects of these two types of gene inactivation, the researchers teased apart two distinct roles of DHR4 in maturation. They found that one effect of DHR4 loss was that larvae of the mutant flies stopped eating too early in development, initiating behaviors that led to early pupa formation. These pupae developed into smaller, lighter adult flies. “These mutants eat and grow normally until their last larval stage,‿ said Thummel, “when they stop eating prematurely and go into metamorphosis earlier than they should.‿

The researchers also found that DHR4 -deficient flies showed defects in the process of metamorphosis itself. These defects involved the developmental “circuitry‿ controlled by the key insect steroid hormone ecdysone, known to be a major orchestrator of biological processes throughout a fly's development and a critical regulator of metamorphosis.

“The discovery of DHR4 's role in repressing the genetic cascade triggered by ecdysone was very gratifying, because it filled in a piece of an important puzzle,‿ said Thummel. “In flies, the work of many laboratories has produced an elegant, detailed model of the developmental machinery triggered by ecdysone. However, there has been one piece missing, which we have been seeking for many years - how the earliest response to ecdysone is repressed.

“These genes switch on and off really fast,‿ explained Thummel. “We knew that ecdysone turns them on, but we never knew what turned them off. Now we know that DHR4 is one of the critical components required for shutting down that response, so proper development can proceed."

[Bradford]: This brings to mind comments of Phil Skell, a retired professor with a PhD in chemistry. Dr. Skell has argued, based on his interviews of researchers, that theories of natural history, including evolution, are irrelevant to modern research and scientific progress. I would concur.

Sunday, June 11, 2006

Generating Multiple Codes through Mutations

From Dembski's blogsite:

June 10, 2006

'Writing Computer Programs by Random Mutation and Natural Selection'

"The first computer program every student writes is called a “Hello World” program. It is a simple program that prints “Hello World!” on the screen when executed. In the course of writing this bit of code one learns about using the text editor, and compiling, linking and executing a program in a given programming environment.

Here’s a Hello World program in the C programming language:


int main(void)
printf(”Hello World!\n”);

This program includes 66 non-white-space text characters. The C language uses almost every character on the keyboard, but to be generous in my calculations I’ll only assume that we need the 26 lower-case alpha characters. How many 66-character combinations are there? The answer is 26 raised to the 66th power, or 26^66. That’s roughly 2.4 x 10^93 (10^93 is 1 followed by 93 zeros).

To get a feel for this number, it is estimated that there are about 10^80 subatomic particles in the known universe, so there are as many 66-character combinations in our example as there are subatomic particles in 10 trillion universes. There are about 4 x 10^17 seconds in the history of the universe, assuming that the universe is 13 billion years old.

What is the probability of arriving at our Hello World program by random mutation and natural selection? How many simpler precursors are functional, what gaps must be crossed to arrive at those islands of function, and how many simultaneous random changes must be made to cross those gaps? How many random variants of these 66 characters will compile? How many will link and execute at all, or execute without fatal errors? Assuming that our program has already been written, what is the chance of evolving it into another, more complex program that will compile, link, execute and produce meaningful output?

I can’t answer these questions, but this example should give you a feel for the unfathomable probabilistic hurdles that must be overcome to produce the simplest of all computer programs by Darwinian mechanisms.

Now one might ask, What is the chance of producing, by random mutation and natural selection, the digital computer program that is the DNA molecule, not to mention the protein synthesis machinery and information-processing mechanism, all of which is mutually interdependent for function and survival?

The only thing that baffles me is the fact that Darwinists are baffled by the fact that most people don’t buy their blind-watchmaker storytelling."

[Bradford]: It baffles me too. I have some additional questions. How does a random generating and selection process produce the encoded conventions required by the C and English languages? There is an epigenetic parallel. "Hello World" is intelligible to those familiar with the alphanumeric code used to express the English language. The computer code is expressed by means of a second and distinct code. If these codes are not generated in the absence of intelligence what assures us the genetic code was?

Friday, June 09, 2006

Is ID Scientific? Is Abiogenesis?

Part of an article published in the 'Star Tribune' and authored by Bruce Simat and Walter Remine appears in this post. The article was once online but is no longer generally accessible at the publisher's website. From the article with my commentary identified:

'Intelligent design is scientific, and evidence favors a designer'

'Intelligent design does offer testable theories.'

'Our View Bruce Simat Walter Remine'

"We were disappointed with the many misunderstandings given in Chris Zerby's article against intelligent design (Jan.4 Star Tribune North). Zerby felt the interview with Bruce Simat (Dec. 21 Star Tribune North) was insubstantial.

However, it was a 90-minute interview, and the brief published excerpts represented the reporter's tastes. Zerby's issues can be answered directly.

The astonishing complexities of the simplest known life-forms strongly suggest a designer, just as something vastly simpler (your car engine) demands a designer. That conclusion is eminently reasonable and moved by the evidence. Just as important, the ID theory -- that an intelligent designer is required for the origin-of-life from nonlife -- is risky and testable. That makes it a scientific theory (under the same criteria used by evolutionists in all their court cases). In fact, it is among the most rigorously tested theories in biology."

[Bradford]: If life is the product of a series of unguided chemical reactions then in an environment in which this occurs life should become an inevitable outcome. Substances and the reactions involving them would be specifiable. There would be a determined aspect to causality enabling its repetition. The presence or absence of this very quality is also the means by which intelligence is either ruled out or identified as a causal agent.

"On the other hand, evolutionists have no scientific theory for the origin-of-life. The simplest known life-forms are vastly too complex to have originated (directly from nonlife) through known processes plus time and chance. That much is acknowledged by evolutionary specialists and would seem to falsify the evolutionary view. To evade such outright falsification, evolutionists splintered into various
contradictory speculations, which claim the first life-form was: 1)only amino acids, or 2) only nucleic acids, or 3) only crystalline clay, or 4) "came from space."

These speculations are not driven by any evidence in their favor. Instead, they attempt to avoid outright falsification of the evolutionary view. Just as importantly, they are not risky or testable. They are convenient stories, with no risk or testability. Thus, concerning the origin-of-life, the evolutionary view is either false or unfalsifiable -- and either way, it is not scientific. Intelligent
design is scientific, and evolution is not -- and this is backward from the usual stereotype."

[Bradford]: In other words the hypothesis that intelligence is a necessary causal component to generating life is falsifiable by an experimental outcome showing that a series of chemical reactions leads to a cell. Proponents of abiogenesis have protected their belief from falsification standards through vagueness that allows faith in unspecified pathways to substitute for tests of the hypothesis itself.

Wednesday, June 07, 2006

The Concern Goes Beyond the Textbook

A controversy is brewing over a biology textbook used at Virginia Commonwealth University. Or perhaps it is better said that an adjunct biology professor is intent on creating a controversy. Part of the article referenced at the following URL is included along with my identified comments.

'June 7, 2006

A Textbook Case

'When teaching evolution in college classrooms, where does creationism fit in? Some VCU professors are wondering.'

by Brandon Walters

"When biology professor Jim Sparks lectures at Virginia Commonwealth University this fall, he’ll spend plenty of time on the missing link. In this case, however, it’s his new textbook.

The 35-year-old adjunct professor is upset about the new text his peers at VCU have chosen for him to use in teaching Biology 101. Sparks says it omits critical chapters in evolutionary theory and is biased toward creationism and intelligent design, which argues life is too complex to have evolved over millions of years solely through Darwin’s theory of natural selection and must have come at the direction of a supreme being or a supernatural force.

The book Sparks faults is “Essentials of Biology” by prolific science writer Sylvia S. Mader and published by the mainstream McGraw-Hill press.

“The text is confusing and minimalist,” Sparks says. “I can’t teach a lecture based on this book.” Describing most introductory biology texts as uniform, Sparks says he first thought the book was just weak. In the beginning, he even gave his blessing when the department allowed his input. But then he actually read the text.

He also soon learned that one of his colleagues who pushed for the book has strong creationist ties and that the text has also been picked up by Oral Roberts University. And in the chapter called “Darwin and Evolution” on page 230, he found a direct reference to the California-based Institute for Creation Research, stating that the organization “advocates that students be taught an ‘intelligent-design theory.’”

[Bradford]: This smacks of academic McCarthyism. A text was "picked up by Oral Roberts University" and a colleague "who pushed for the book has strong creationist ties" is meant to do what- discredit the book? It may have that effect but if it does it runs counter to the spirit of academic freedom that should pervade Sparks's world. One's "creationist ties" should be utterly irrelevant but sadly that is not the case.

Even though the book clearly states that intelligent-design theory does not meet the test of scientific theory, despite that nearly half of all Americans believe the Old Testament account of creation, Sparks says the mention of the institute is disturbing. “It’s product placement,” he says, “like when Tom Cruise drinks Pepsi in the ‘War of the Worlds.’”

[Bradford]: Sparks's product placement charge is not backed by anything disclosed in this article. There is missing context. Evidently Sparks would like nothing better than to censor mention of the Institute for Creation Research. That's consistent with policing thought.

Some of his colleagues say he’s paranoid and making much ado about nothing. But Sparks may have a point, according to some people following the debate over how evolution is taught nationwide in grade schools and institutions of higher ed."

[Bradford]: If Sparks would confine his objections to the information contained or not contained in the book he might have a point worth listening to but he conveys an unhealthy interest in ideology when he goes beyond this.

"Sparks insists VCU and its students are getting ripped off. When he tried to use his previous syllabus to create a new one for the Mader text, he says he couldn’t because critical elements of evolution were missing from the book.

For example, the Mader book doesn’t mention a concept called abiogenesis or the Miller-Urey experiment, which posits that life may have originated from simple amino acids and nucleotides being synthesized by exposing the earth’s early gaseous atmosphere to electric charge and UV radiation. The hypothesis, now contested, remains a standard part of biology curricula."'

[Bradford]: We are better off for the absence of this unscientific belief. There is more evidence that proteins and nucleic acids do not arise outside a cellular environment than there is scientific evidence for life arising. The fact that this would be raised as an objection only reinforces the impression that Sparks's interests in the textbook go beyond legitimate scientific concerns.

Intelligent Design Leads to...

Scientist and educator Jerry Bergman hits the nail on the head with this article accessed at the provided URL. The logic makes sense to all sides. "Critical analysis of evolutionism leads to intelligent design, which leads to the Creator requirement. The Creator requirement leads to religion, which leads to God." At this point the establishment clause is invoked to short circuit this chain of logic before it gets the chance to get untracked. The establishment clause may be the most abused judicial doctrine in the USA. It rests largely on selective use of founding father statements (primarily those of Jefferson) from an ideological group that generally resists the idea that initial intent be a restrictive guideline in interpreting the constitution. The article:

Intelligent design leads to forsaking atheism
By Jerry Bergman
Northwest State College

Why did the court rule against teaching intelligent design in the Dover, Pa., case? Judge Jones’ ruling was summed up by one commentator as follows: Critical analysis of evolutionism leads to intelligent design, which leads to the Creator requirement. The Creator requirement leads to religion, which leads to God. The courts have consistently ruled that the state cannot hinder or aid religion – and that teaching intelligent design aids religion.

Of the many examples I know of people who left atheism and became theists because of intelligent design, I will cite only two.

Antony Flew, professor emeritus at Reading University, was a leading 20th-century intellectual and author of many books including “Atheistic Humanism.” Although as a youth Flew was a devoted Christian, during his teens he rejected Christianity because of his study of Darwinism. He concluded that evolution could fully account for the creation of all life – and that no need existed for a Creator who had been put out of work by science. Flew eventually became a leading defender of atheism for over half a century.

Flew kept reading and thinking about this topic, though, and eventually came back to the theism of his youth. His conversion was primarily because of his study of intelligent design. As he told The Associated Press, his views were now similar to the “American ‘Intelligent Design’ theorists who see evidence for a guiding force in the construction of the universe.” Michael Behe’s and William Bembski’s books were especially influential. Flew added that an argument from design, “assures us that there is a God” and that DNA research has provided us with “a new and enormously powerful argument” for design. Flew stresses that the main reason for “believing in a First Cause God is the impossibility of providing a naturalistic account of the origin of the first reproducing organisms.” He states that his whole life has been guided by the principle of Socrates, “follow the evidence where it leads” and, in this case, it led him to theism.

The second is Harvard Medical School professor Dr. Timothy Johnson. Johnson is most well-known as an ABC News medical correspondent, and for his many documentaries. His new book on intelligent design titled “Finding God in the Questions,” a New York Times best-seller, both defends intelligent design and reviews his own spiritual journey beginning from his childhood religious beliefs to his acceptance of skepticism, then back to belief. He discusses in detail why, as a scientist, intelligent design was critical in his journey from agnosticism to belief.

Johnson graduated from high school as valedictorian and, after two years of college, decided to become a minister. His theology studies at the University of Chicago, instead of deepening his faith, caused him to lose it. In his words, “under the challenge of some very bright and skeptical teachers at the University of Chicago” he began to “doubt most everything” he had learned. This included the belief that the Bible was God’s word, that Jesus was God’s son, and that God rules the universe. No longer a believer, he graduated and was ordained but did not enter the ministry. He elected to study medicine, partly because of his seminary field placements in hospitals.

He came to believe in God only after many years of examining in detail the major questions that trouble many of us. He began by questioning the evolutionary belief that the universe is a product of only time, natural law, and chance. After extensively studying the scientific research, especially intelligent design, Johnson concluded that our inner and outer universes are not only far too vast and complex to be the result of natural forces but are constructed so as to force the conclusion that they were created by an intelligent designer. Johnson concluded the footprints are found everywhere, from the human conscience to our basic need to form the complex social relationships that shape our lives.

Johnson cites the major intelligent design literature, which he recommends highly. His journey parallels that of many people today and is why intelligent design has been a major means for many to convert from atheism to theism, and why courts rule teaching it is religious advocacy. The above are only two case histories involving conversion from atheism to theism because of intelligent design discussed in a book I edited that will be published this fall by Master books.

Monday, June 05, 2006

Evidence for ID

Patience is very much a virtue when exchanging views with internet Darwinists who mistake Darwinian concepts for sound scientific evidence. This from another CAID post:

>What you didn’t understand then, and you still don’t understand now, is that ID, as a theory, cannot “win” by default. Unless and until you all can cough up something resembling evidence for your theory - something more substantive than a list of neo-Darwinian concepts that you don’t personally understand, that is - there’s no reason to subscribe to ID as a theory.

Bradford: One indication of an effect resulting from intelligence is that the effect would not occur in the absence of intelligence. Evaluating current origins theories and finding them wanting is a first step toward an intelligent inference. On the other side of the coin IDers should follow a pattern established by Darwinists. Darwinists have used an argument from analogy as positive evidence for common descent. They first looked at similar morphologies and later at shared genomic features and concluded that the similarities would be what is expected of an evolution paradigm and hence would be evidence for common descent.

What's good for the goose is good for the gander. IDers examine the pre-established encoding conventions enabling protein translation as well as self-correcting genomic features found in even relatively "simple" unicellular organisms and conclude that encoded means of transmitting genetic information combined with a mechanism that prevents the corruption of that code is what is expected of an intelligent causal paradigm and is hence evidence for intelligent design.

More on the CAID exchange

This is a fairly typical presentation of an internet Darwinist complete with shifting positions and unsubstantiated claims. As continued from the last post:

As I said useless garbage. Cells cleave and degrade non-functional proteins.

There’s no “cell” involved here. This is a simple self-replicating polyeptide. The process of replicating itself does not produce “useless garbage” - it produces more copies of this protein.

Bradford: Which are useless to any life creating process. You can take all the proteins an organism requires place them in an aqueous solution and you have nothing more than wet proteins. Life requires more than peptides. You don't get nucleotides from replicating peptides.

What selective advantage produces a cell from a peptide with 32 residues?

Who said anything about cells? This is really primitive life here. If you think really primitive life resembled anything as complex as a “cell”, it’s up to you to explain why.

Bradford: There is no such thing as really primitive life except in your imagination. It is not an experimental result but rather something you believe in based on faith.

As I’ve said repeatedly - and this will be the third time - selection operates on the reproduction of such a protein.

Bradford: Real researchers can specify what they mean by a selctive advantage when referencing a protein or gene. Apparently you can do nothing other than assert that selection operates.

For the third time - in this very post, no less - there is no “cell” here.

Bradford: Now you're getting it. There is no evidence that cells arise other than in the imaginations of Darwinists.

Please try to deal with the things I actually post, rather than whatever it is your fevered imagination thinks I’ve posted.

Bradford: You post nothing but unsubstantiated claims trying to link a peptide to another peptide. This is a theoretical stuttering problem not anything of scientific value.

I realize it’s much easier for you to invent things for me to present, so that you might knock your own softballs out of the park with some sort of canned refutation, but it really does betray just how little you are interested in an actual, honest exploration of these questions.

Bradford: I'm interested in honest scientific evidence not stories about vague peptide pathways.

It affects the issue of life’s origins. ID encompasses the whole of natural history.

Great - biogenesis, “a-” or otherwise, is your problem then. You figure it out. As I’ve said, the theory of evolution is not dependent on any particular biogenetic scenario - if your theory is, better get crackin’.

Bradford: Then students need to be taught that there is no scientific mechanism showing how life originated and that Darwinism is based on an unsupported assumption about the sufficiency of naturalism.

What constitutes a “bad copy” in an extra-cellular environment?

You’re kidding, right? A copy that’s not identical to the original and is not capable of self-replication as a result is a “bad” copy. A copy that is identical to the original and is hence also capable of self-replication is a “good” copy. A copy that is not identical to the original but is still capable of self-replication is a “good enough” copy.

Bradford: You never did address the issue of where a steady supply of 20 L amino acid isomers come from.

Bradford: What research paper indicates that “good copies” of a 32 residue peptide lead to functional cellular proteins?

Burn, strawman, burn! These are one-offs, William - you’re talking about what are likely singular events in the history of the world.

Bradford: I'm talking about experimental evidence to back up your replicating peptide claims. Replicating peptides do not produce nucleic acids; an essential biochemical. It's a matter of simple biochemistry having nothing to do with singular events.

ID claims such things are impossible. For ID to be refuted, then, all one must do is show that it’s possible, no matter how unlikely. Enjoy your stay in what is exceedingly likely to be a continuously shrinking box.

Bradford: The more we learn about the details of cellular functions the more obvious it becomes that cells do not arise from prebiotic soups. But you are entitled to your unscientific beliefs that they do.

A replicating peptide in a precellular environment is an abiogenesis scenario. I thought you knew the difference between evolution and abiogenesis.

Uh, no, it’s not an abiogenetic scenario. If I asserted that this peptide were the first such thing, with no self-replicating precursors, and I set out to tell you where, how, and when such a thing came about, sui generis as it were, that would be an abiogenetic scenario. Since I’ve said none of those things, this is not a theory of abiogenesis - it is merely an examination of a simple self-replicating polypeptide.

Bradford: It's nothing more than an indication that peptides can replicate under specified conditions as long as an adaquate supply of amino acids exists. Taking it any further than that is a gigantic leap of faith.

CAID Exchanges

This is from a post at the CAID comment section involving an exchange in which my comments are identified. Incidentally, when I access the website my posts appear in extremely small letters. I was informed that this not Aleph's experience. It is only the CAID website where this occurs for me. Does anyone else have this experienece? From the site:

Bradford: I wrote ‘biological purpose’ but then you read what you want a sentence to say.

Okay, fine - the universe is also not obligated to satisfy your sense of “biological purpose” either. It replicates, and that’s enough for natural selection to act on it.

Bradford: Biological functions are objectively measurable. It's not a matter of what my sense of it is. Natural selection is based on the belief that any biological system that confers a selective advantage will be retained by an organism. What selective advantage produces a cell from a peptide with 32 residues? Where do you get a functional genome from this?

Self-replicators that form bad copies are
likely to produce non-functional offspring.

Bradford: What constitutes a "bad copy" in an extra-cellular environment?

Self-replicators that form good copies are likely to produce functional copies.

Bradford: This is idiocy. What research paper indicates that "good copies" of a 32 residue peptide lead to functional cellular proteins? Where do nucleotides and phosphate groups come from? Give me a scientific response rather than silly assertions.

Really, these are not exceedingly difficult
questions, nor are they especially novel.

Bradford: The only answers you've provided involve waving a replicating magic wand in place of descriptions of real biochemical pathways.

Perhaps you'd be better off learning a bit about
evolution before we proceed

Bradford: A replicating peptide in a precellular environment is an abiogenesis scenario. I thought you knew the difference between evolution and abiogenesis. Do you need a basic biochemistry primer?

Saturday, June 03, 2006

A Legal Battle Over Stickers

The founding fathers would not have dreamed federal judges would issue rulings based on their hostility toward Christians and justify it based on the beliefs of those same founding fathers but this is what it has come to. From the referenced site:

"The stickers contained the true statement that “evolution is a theory, not a fact” and nothing about any religious faith. A federal court judge agreed that the stickers were not applied to the textbooks for a religious purpose and were devoid of religious content. Nonetheless, he deemed the stickers a violation of the so-called “separation of church and state” for the sole reason that many people were aware that Christians liked the stickers."

[Bradford]: Abuse of the "establishment clause" is epidemic. The establishment clause concept has become a tool used by legislating judges to limit the influence of conservative Christians. The argument that the meaning of the word 'theory' is misunderstood is inconsequential. You don't issue constitutional rulings based on the understanding of those advocating use of the phrase. Not if you have judicial integrity and respect for free speech.

“The district court’s decision seriously misstates the law. Are we really going to start declaring laws unconstitutional just because Christians happen to support them?” asked ADF Senior Legal Counsel Kevin Theriot. “No federal court has ever declared something unconstitutional just because it believes a general awareness exists that Christians are in favor of that thing.”

According to the brief filed today, “The District Court’s analysis will lead to absurd results…. The Establishment Clause was never meant to prohibit the passage of a secular law, for a secular purpose, simply because Christians actively lobbied for the law.”

[Bradford]: The real bone of contention is the second part of the statement indicating that evolution is "not a fact." Evolution has become a sacred cow. You don't criticize sacred cows without consequences.

Expanding the Boundaries of Science

A worthwhile article entitled 'Darwin’s Divisions The Pope, the Cardinal, the Jesuit & the Evolving Debate About Origins' was authored by Martin Hilbert in 'Touchstone.' The entire article can be accessed at the following site:

A small part of the article is quoted and my comments included. From the article:

"That is Coyne’s first mistake. The second is more substantial. The main problem with his argument is not his attempt to claim papal authority for neo-Darwinism, but his attempt to portray science as a religiously neutral enterprise and at the same time as the ultimate basis for a rational worldview.

“Science,” he declares at one point, “is completely neutral with respect to philosophical or theological implications that may be drawn from its conclusions.” Yet he goes on to say that science has a bearing on our understanding of divine omnipotence and omniscience. So is it neutral or is it not? He informs us that “in the universe as known by science, there are essentially three processes at work: chance, necessity, and the fertility of the universe.”

[Bradford]: Fertility of the universe? While Coyne's views are not presented as representing a scientific consensus they do indicate confusion as to the distinction between conclusions supported by scientific data and ontological beliefs referencing such data. When scientists venture into the ontological realm and advance their personal views with "scientific claims" they invite criticism for they have strayed beyond their turf.

"Let us begin with chance and necessity. If this is a statement of scientific methodology, very well and good. Science tries to explain the realities of this world in terms of other realities in this world. It looks for patterns and demands that experiments adduced in favor of theories be replicable. Any given situation in nature is assumed to unfold by necessity: Identical initial conditions must lead to the same outcomes. It does not include any personal element, such as divine intervention. Science as we know it could only begin when the denizens of Mount Olympus ceased to count as explanations for natural phenomena."

[Bradford]: If identical initial conditions lead to the same outcome then what conditions and what chemical reactions could possibly give rise to an encoded genome capable of being expressed and replicated? The standard response is a variation of "we are researching the unknown for answers." One problem with this is any selection paradigm operating in conditions thought to resemble those on prebiotic earth must operate outside the currently accepted Darwinian framework encompassing observable biological systems. One can explain the selective value of any particular gene once its function is understood. The function supports a larger biological entity which is eventually the organism itself. Function and therefore selective value are inseparable from the larger system i.e. the containing organism. So then what would be the selection criteria describing chemical reactions leading to a functional encoded nucleic acid in a prebiotic world still devoid of such biochemicals? The question seeks not simply an unknown. Rather, it points to an existing theoretical framework as an inadaquate tool within which to search for answers.

Thursday, June 01, 2006


From the referenced site. Commentary follows.

'New Scientist'

'Article Preview
Review: Flock of Dodos: The evolution-intelligent design circus
03 June 2006
Amanda Gefter
Magazine issue 2554'

"At last, a documentary that gives us the chance to chuckle at the controversy that has been consuming biology teaching in the US, says Amanda Gefter AT FIRST glance, the so-called debate between evolutionary scientists and supporters of intelligent design is not very funny. But after endless discussions in the media about pseudoscientific concepts such as the "irreducible complexity" of structures like the flagella of bacteria, we could all use a good laugh. So we should thank evolutionary ecologist and film-maker Randy Olson for his documentary Flock of Dodos, which premiered last month at New York's Tribeca Film Festival.

Olson travelled around the US talking to people on both sides of the argument. What he discovered is that the debate is not about facts, it is about people. As you would expect from someone who studied at Harvard under Stephen Jay Gould, Olson treats the theory of evolution as it ought to be treated: as a long-standing explanatory framework supported by an immense amount of hard evidence. The crucial question, then, is why do so many ..."

[Bradford]: The article continues and is accesible to subscribers. In this brief snippet though the author put forth familiar criticisms indicating that she, like many others, either does not understand the term irreducible complexity or does not appreciate the inability of the theory of evolution to explain how basic and universal biological systems, fitting the definition of irreducible complexity, evolved. Why limit our focus to the bacterial flagellum? Why not take a look at a universal irreducibly complex system that enables the synthesis of the proteins found in all systems and all organisms. The pseudoscientific reference indicates that accounting for its evolution should be a piece of cake particularly given the author's claims about the "long-standing explanatory framework supported by an immense amount of hard evidence" that is said to describe evolution. The protein synthesis function can be broken down into an analysis of transcription and translation sub-functions. Among the biochemical components is a complex of proteins essential to protein synthesis and a variety of RNA and of course the transcribed DNA. The multiple interacting parts to this functional system fits the term irreducibly complex which is nothing more than a descriptive phrase. Whether an evolutionary path to a particular irreducibly complex biological system is supported by evidence is a separate issue. Are there any non-pseudoscientific pathways to the protein synthesis function? Given the bombast and arrogance that typically characterizes Darwinian approaches to Behe's irreducible complexity, one would expect ready answers to questions as to how basic cellular functions and biochemical pathways evolved. Did the protein synthesis function evolve gradually through incremental steps; each one providing the next link in the chain? Is that an apt analogous device?

Precursor systems were a catch phrase used to answer the question of how the bacterial flagellum evolved. What were the precursors to amino acyl tRNA synthetases? There must have been some right? What were they and what is the evidence supporting the answer?

I do not know Amanda Gefter and will make no comment about her but in general I wonder how well many writers understand basic biochemical and cellular biology concepts. Do many appreciate the specificity between protein binding sites and their ligands? If they do what selective process do they cite for the evolution of RNA polymerases and amino acyl tRNA synthetases? What was the sequential evolution of the protein and nucleic acid components of the protein synthesis function? Most of all I would like to know what supporting evidence assures them that any process- evolutionary or not- was devoid of an intelligent causal component? Running to the Randy Olsons of the world for reassurance is a poor substitute for scientific evidence.