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Thursday, June 05, 2008

The God of the Chaps - the ones who should retire soon

Here's an informative article, "God and Evolution" by Avery, Cardinal Dulles in First Things (October 2007) that offers an explanation of discomfort with intelligent design theory:
An important school of scientists supports a theory known as Intelligent Design. Michael Behe, a professor at Lehigh University, contends that certain organs of living beings are “irreducibly complex.” Their formation could not take place by small random mutations, because something that had only some but not all the features of the new organ would have no reason for existence and no advantage for survival. It would make no sense, for example, for the pupil of the eye to evolve if there were no retina to accompany it, and it would be nonsensical for there to be a retina with no pupil. As a showcase example of a complex organ all of whose parts are interdependent, Behe proposes the bacterial flagellum, a marvelous swimming device used by some bacteria.

Fine, but then he says,
At this point we get into a technical dispute among microbiologists that I will not attempt to adjudicate. In favor of Behe and his school, we may say that the possibility of sudden major changes effected by a higher intelligence should not be antecedently ruled out. But we may take it as a sound principle that God does not intervene in the created order without necessity. If the production of organs such as the bacterial flagellum can be explained by the gradual accumulation of minor random variations, the Darwinist explanation should be preferred. As a matter of policy, it is imprudent to build one’s case for faith on what science has not yet explained, because tomorrow it may be able to explain what it cannot explain today. History teaches us that the “God of the gaps” often proves to be an illusion.

What Cardinal Dulles does not seem to grasp is this: Once you decide that materialist explanations should be preferred, they are preferred even when the evidence supporting them is much poorer than the evidence supporting other explanations. That's because it's not a level playing field, right?

Thus, to take the flagellum as our example (because he and Behe both do), any idle conjecture about how it might have all happened by chance is "science" and any critique of such conjecture, however based, is "religion" (and therefore can't be published in a science journal?)

The "God of the Gaps" is a convenient fiction by which science-and-religion profs avoid facing the uncomfortable reality that most of what they do has been rendered irrelevant by the growing failures of Darwinism and materialism. No one needs them to cushion the pain of discovering that these things are true, because they're not. And increasing numbers of people know that.


And what's so bad about machines anyway?

Some people were not amused by my review of Christoph, Cardinal Schoenborn's book, Chance or Purpose?

One thing I had found surprising (and didn't make a secret of the fact) was the Cardinal's distaste for the idea that life forms could be compared with machines. He blamed the ID guys for that idea, which will be news to most biochemists.

Meanwhile, some people insist that only deists (people who think there is maybe a sort of God who wound up the world and let it go, but that's all, really) think that the design of life involves machines. Therefore it is a Bad Idea.

In reality - whatever we want to make of it - many elements of our physical life are much more like machines than they are like anything else. I have been reading Mike Gene’s book, The Design Matrix: A Consilience of Clues, which sets that out in detail. I strongly recommend Gene's book. By all means, sell your deluxe edition of Darwin's Origin of Species - with the gold-leafed illustration of “Ye Tree of Life” - and buy this one.

Here, for example, are some of the protein machines inside cells:

Examples: DNA processing machines

Replisome – replicates and repairs DNA (includes sliding clamps and clamp loaders)

Helices – unwinds and separates strands of DNA

Topoisomerase – untangles DNA strands that get knotted

Rad50 and RecA – fix DNA damage

RNA processing machines:

Transcriptosomes – massive complexes that make RNA copies of DNA genes

Splicesome “The function of the spliceosome is to cut the RNA into pieces, remove the sequences that are not part of the instruction for protein synthesis and splice he instruction pieces back together.” (Considered the most complex machine, 140 proteins, five RNA molecules.)

Editosome – “protein machines with more than twenty parts which function carefully select and precisely edit the protein synthesis instructions inherent in the ERNA molecule.”

Degradosomes and exosomes – degrade the RNA molecules when there is a problem with the instructions or when they are no longer needed.

(From pp. 90-91, but otherwise on and on)
Basically, it doesn’t matter what the Cardinal or the Deists or anybody at all think about machines.


Life is instantiated in machines. Any theory of life needs to just accept that and move on.

Re not liking the idea that our cells contain zillions of little machines: Years ago, an Ontario farmer was approached by someone who was upset by the fact that hens (like all birds) have only one orifice for the ejection of all body wastes, as well as for the laying of eggs.

He suggested that that individual complain to The Manufacturer ... Anti-Machinists may wish to do the same.

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Canada chronicles: Biology in the wrong hands?

Shortly after the Expelled film (about the intelligent design guys) hits Canada this summer, this fall CTV is producing Eleventh Hour, "a drama from Jerry Bruckheimer about what happens when biology is placed in the wrong hands." Stars Rufus Sewell.

Now, is this going to be "Honey, I shrunk the crowd at the Tim Horton's ... quick, give me one of those baggies!" or is it going to be "If Darwin was wrong, we're all doomed!" If the latter, yawn.

I can't currently find out much about it, but Bruckheimer has a respectable reputation as a sci-fi producer so one can hope for the better idea.


Changes of last 10 000 years too great to be explained by Darwinian mechanism?

Here's a 2005 article by Eric Hobsbawm defending history, "It is fashionable to say 'my truth is as valid as yours'. But it's not true".

Hobsbawm is defending Marxism, and it is hard to imagine a political system more exploded than Marxism (though its professors are busy chipping away at civil liberties wherever they can).

But curiously, he says,
DNA analysis has established a firmer chronology of the spread of the species from its original African origin throughout the world, before the appearance of written sources. This has both established the astonishing brevity of human history and eliminated the reductionist solution of neo-Darwinian socio-biology.

The changes in human life in past 10,000 years, let alone the past 10 generations, are too great to be explained by a wholly Darwinian mechanism of evolution via genes. They amount to the accelerating inheritance of acquired characteristics by cultural and not genetic mechanisms.

What he is saying is that trying to figure out what Alley Oop might have done or why he might have done it 20,000 years ago is not a useful approach to understanding life today. That is probably true, even if a Marxist says it. But then, of course, he goes on to say,
In short, the DNA revolution calls for a specific, historical, method of studying the evolution of the human species. It also provides us with a rational framework for a world history. History is the continuance of the biological evolution of homo sapiens by other means.

which leads me to wonder, naturally enough, what "other means" he has in mind. He also insists,
Secondly, the new evolutionary biology eliminates the distinction between history and the natural sciences and bypasses the bogus debates on whether history is or is not a science. (Eric Hobsbawm is author of The Age of Extremes: The Short 20th Century 1914-1991. This is an edited extract from a speech to the British Academy Colloquium on Marxist historiography, first published in Le Monde diplomatique )

Why is a debate on whether human history is a science bogus? Actually, that is an important question, and a lot is at stake. In any event, if human history is not a science, then evolutionary biology is not a science either. I happen to think that neither is a science for that exact reason. But that doesn't mean that neither is a source of useful information. If I want to know what happened during World War II, I consult a historian, and expect factual answers. And the historian's information is not rendered more accurate by describing it as a science.

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Intelligent design research: Using Chinese anagrams to model proteins

The Biologic Institute (an ID research center) has a paper published in PLOS One, an on-line peer-reviewed journal: Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints, by Douglas D. Axe*, Brendan W. Dixon, and Philip Lu. Biologic Institute, Redmond, Washington, United States of America

It's a computer program that offers Chinese anagrams to try to model the awful complexity of proteins. From the paper:

Although the Han characters all originally functioned as stand-alone words, the number of concepts needing words has increased dramatically since the character set became effectively fixed. Instead of inventing new characters, the solution was to combine existing characters to form multi-character words, which are now common. These words are like multi-protein complexes in that their function requires correct arrangement of two or more parts. However, while protein complexes are compound structures, multi-character words are separate structures arranged sequentially. The next section explains how this is implemented in the vector world and considers the implications for functional constraints.

High-level functions: From sentences to texts, and operons to proteomes. In both biology and language, the jump from elementary function to useful function brings with it a new level of complexity. Words are elementary semantic units, in that meanings are attached to symbols starting at the word level. But language only becomes useful for communication when word-level meanings are combined to convey more complex meanings. Similarly, although proteins and protein complexes perform low-level functions of biological relevance, organismal capabilities—from survival-enhancing phenotypes all the way up to survival itself—require the coordinated combination of many such functions. Ultimately whole proteomes are coordinated in this way.

I was going to try to copy some of the illustrations but the best I can do for now is link you to the slide show.

Here's a comment from a mailng from the Discovery Institute:
Chinese writing, in particular, employs structural characters that are analogous in some interesting ways to protein structures. Like folded proteins, these written characters perform the low level functions from which higher functions can be achieved.

Stylus builds on this analogy by using a life-like genetic code to specify simple building blocks (twenty vectors, analogous to the twenty amino acids) that in turn build Chinese characters. In this way, gene sequences looking very much like biological sequences encode vector chains with two-dimensional shapes. If those chains have the right geometry, by conforming to the shape of a character, they provide basic semantic function. And the functional hierarchy builds up from there.

The result is an artificial genetic system where genes encode basic functions by means of appropriate structures, and genomes encode higher functions that employ these basic functions. So, if it can be written in Chinese, it can be encoded in a genome and represented in working form by a proteome.

The big question, of course, is whether Darwinian evolution can do anything interesting in a system like this. In view of its similarity to life, the answer would be hard to ignore either way.

And the truth is—we don’t know the answer. Yet.

Guess someone will have to lean on PLOS One to take this paper down. Meanwhile, here's the abstract:

The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions—relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure–function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure–function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector proteins by evolving successive lines from a single starting gene. These homologues show sequence and structure divergence resembling those of natural homologues in many respects, suggesting that the system may be sufficiently life-like for informative comparison to biology.


My review of Christoph, Cardinal Schoenborn's attempt to tiptoe quietly through the intelligent design controversy

His attempt to tiptoe quietly is better known as his book, Chance or Purpose? Creation, Evolution, and a Rational Faith (San Francisco: Ignatius Press, 2007).

Tiptoeing quietly won't work, actually. The ID guys don't really care what he says because Darwinism and materialism are toast so burnt that even a miracle couldn't revive them, not that any miracle worker would bother, of course. But the Darwinists/materialists are accustomed to demanding total surrender from everyone for no particular reason, and I guess it becomes a habit or something. Anyway:

Introduction Christoph Cardinal Schoenborn's Chance or Purpose? Flickering light on the ID controversy at best

Part One: Is the proposed distinction between evolution and "evolutionism" legitimate in today's environment? (Of course not.)

Part Two: Why is it called "intelligent design" instead of "intelligent intervention"? (Because design is essential and intervention is optional.)

Part Three: What Cardinal Schoenborn doesn't like about intelligent design (The ID guys talk as though cells operate like machines or something. News flash!: They do. )

Part Four: Can the disgraced Teilhard de Chardin evolve into a pioneer of faith? (People just wouldn't get Christ the "evolutor" at my parish, no matter who said it?)

Part Five: Darwin's ladder knocking over Jacob's ladder? (Well, that's the idea anyway, and it won't be the Darwinists' fault if it never happens.)

You can read some comments and my responses here.

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