Research on Intelligent Design

To put together scientific advances from the perspective of Intelligent Design.

Friday, October 07, 2005

Intelligent Design's Theory of Organismal Problem-Solving (TOPS)

Using Intelligent Design Theory to Guide Scientific Research, by Jonathan Wells, PCID 3.1.2, Nov. 2004 (in PDF)

"Intelligent Design theory (ID) can contribute to science on at least two levels."

"On one level, ID is concerned with inferring from the evidence whether a given feature of the world is designed. This is the level on which William Dembski's explanatory filter and Michael Behe's concept of irreducible complexity operate. It is also the level that has received the most attention in recent years, largely because the existence of even one intelligently designed feature in living things (at least prior to human beings) would overturn the Darwinian theory of evolution that currently dominates Western biology."

"On another level, ID could function as a "metatheory," providing a conceptual framework for scientific research. By suggesting testable hypotheses about features of the world that have been systematically neglected by older metatheories (such as Darwin's), and by leading to the discovery of new features, ID could indirectly demonstrate its scientific fruitfulness."

Theory of Organismal Problem-Solving

"TOPS suggests how ID could lead to new hypotheses and scientific discoveries."

"TOPS begins with the observation that the evidence is sufficient to warrant at least provisional acceptance of two propositions:

(1) Darwinian evolution (the theory that new features of living things originate through natural selection acting on random variations) is false, and

(2) ID (the theory that many features of living things could only have originated through intelligent agency) is true."

"TOPS then explicitly rejects several implications of Darwinian evolution. These include:

(1a) The implication that living things are best understood from the bottom up, in terms of their molecular constituents.

(1b) The implications that DNA mutations are the raw materials of macroevolution, that embryo development is controlled by a genetic program, that cancer is a genetic disease, etc.

(1c) The implication that many features of living things are useless vestiges of random processes, so it is a waste of time to inquire into their functions."

"Finally, TOPS assumes as a working hypothesis that various implications of ID are true. These include:

(2a) The implication that living things are best understood from the top down, as irreducibly complex organic wholes.

(2b) The implications that DNA mutations do not lead to macroevolution, that the developmental program of an embryo is not reducible to its DNA, that cancer originates in higher structural features of the cell rather than in its DNA, etc.

(2c) The implication that all features of living things should be presumed to have a function until proven otherwise, and that reverse engineering is the best way to understand them."

"... Take, for example, research on the vast regions of vertebrate genomes that do not code for proteins. From a neo-Darwinian perspective, DNA mutations can provide the raw materials for evolution because DNA encodes proteins that determine the essential features of organisms. Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or "junk DNA." From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much "junk." It is much more likely that noncoding regions have functions that we simply haven't discovered yet."

"Recent research shows that "junk DNA" does, indeed, have previously unsuspected functions .. its results came as a complete surprise to people trying to ask Darwinian research questions."

"The fact that "junk DNA" is not junk has emerged not because of evolutionary theory but in spite of it."

"TOPS and Cancer
.. I quickly learned from reviewing the recent scientific literature that cancer is not correlated with any consistent pattern of DNA mutations, but it is correlated with abnormalities at the chromosomal level -- a phenomenon called "chromosomal instability" (Lengauer et al., 1998). Chromosomal instability, in turn, is correlated with centrosome abnormalities -- particularly the presence of extra or enlarged centrosomes. A growing number of researchers regard cancer not as a DNA disease, but as a "centrosomal disease" (Brinkley and Goepfert, 1998; Pihan et al., 1998; Lingle and Salisbury, 2000)."

"In 1985, I had published a hypothesis about how centrosomes might produce a force in dividing cells that pushes chromosomes away from the spindle poles (Wells, 1985)… In 2002 it occurred to me... Centrosomes that are too numerous or too large would produce too strong a polar ejection force, damaging chromosomes and leading to chromosomal instability."

"If the polar ejection force were really the link between centrosomes and cancer, however, and the polar ejection force were due to a vortexer-like motion of spindle microtubules, what could be the mechanism producing this motion? My attention quickly turned to centrioles."

"Centrioles might be the source of the polar ejection force, and they might hold the clue to understanding cancer."

"In the electron microscope, centrioles look like tiny turbines. Using TOPS as my guide, I concluded that if centrioles look like turbines they might actually be turbines. I then used reverse engineering to formulate a testable, quantitative hypothesis linking centrioles, polar ejection forces, and cancer."

"Centrioles as tiny turbines"

"If the helix inside a centriole rotates like the central apparatus of an axoneme, it could function as an "Archimedes' screw," a corkscrew-action pump that would draw fluid in through the proximal end and force it out through the triplet-microtubule turbine blades."

"By analogy with the central pair apparatus in axonemes, the helix inside a centriole would presumably rotate at about 100 Hz."

"Dynamics of a centriole pair"

"These characteristics are consistent with a model in which the subdistal appendages form a bearing connected to the cell's cytoskeleton, and the distal appendages form a flange holding the mother centriole in its bearing."

Figure 1. Cross-section of a centriole pair. (M) Mother centriole. (D) Daughter centriole. Note the internal helices in each. (a) Subdistal appendages. (b) Spindle microtubules (which are anchored to the subdistal appendages). (c) Distal appendages. In the hypothesis presented here, the subdistal appendages function as a bearing and the distal appendages function as a flange. The large ellipse is the centromatrix capsule enclosing the centriole pair.

"The daughter's torque would thereby cause the centriole pair to revolve eccentrically, producing a wobble resembling the motion of a laboratory vortexer."

"With power being continually supplied by the helical pump inside the mother centriole, calculations show that the centriole pair could reach an angular velocity of more than 10 kHz midway through cell division."

"Centrioles and the polar ejection force"

"Just as a vortexer imparts its wobble to a test tube placed in it, so the centrosome would impart its wobble to the microtubules emanating from it."

"Objects within the spindle would then undergo high frequency, small amplitude circular movements perpendicular to polar microtubules, as originally proposed by Wells (1985)."

"The conical arrangement of the microtubules would convert part of this to a component parallel to the spindle axis, producing a smaller force tending to move objects radially away from the pole. The wobble produced by a revolving centriole pair could thereby generate a polar ejection force."

"Implications for cancer"

"... the presence of too many centriole pairs at either pole could result in an excessive polar ejection force that subjects chromosomes to unusual stresses that cause breaks and translocations. Even more serious than the presence of extra centrioles would be a failure of the control mechanisms that normally shut down centriolar turbines at the beginning of anaphase, since centriole pairs would then continue to accelerate and generate polar ejection forces far greater than normal."

"If the helical pump inside a centriole is driven by dynein, then a rise in intracellular calcium concentration could shut it down."

"If centrioles generate a polar ejection force, the correlation between calcium and vitamin D levels and cancer could be a consequence -- at least in part -- of the role of calcium in turning off centriolar turbines at the onset of anaphase."

"In the hypothesis proposed here, a centriole is a tiny turbine composed of triplet microtubule blades and powered by an internal helical pump. This is the reverse of Stubblefield and Brinkley's idea [1967] that the triplet microtubules turn the internal helix."

"Bornens (1979) suggested that rapidly rotating centrioles, powered by an ATPase in cartwheel structures at their proximal ends, function like gyroscopes to provide an inertial reference system for the cell and generate electrical oscillations that coordinate cellular processes. In the hypothesis proposed here, rapidly rotating centrioles would produce small-amplitude, high-oscillations in spindle microtubules that are mechanical, not electrical as Bornens proposed."

"There are several ways to test this hypothesis. Two ways are:

It should be possible to detect oscillations in spindle microtubules early in prometaphase by immunofluorescence microscopy and high-speed camera technology.

It should be possible to regulate the polar ejection force by raising the concentration of intracellular calcium during prometaphase or blocking its rise at the beginning of anaphase.

If the hypothesis presented here withstands these and other experimental tests, then it may contribute to a better understanding not only of cell division, but also of cancer."

Early reference:

Wells, J., 1985. Inertial force as a possible factor in mitosis. BioSystems 17, 301-315.

Jonathan Wells' responses:

"Concerning my hypothesis that centrioles generate the polar ejection force (PEF) and that an excessive PEF causes chromosomal instability, .. I am not aware that anyone has previously proposed a link between (a) centrioles and PEF, or (b) excessive PEF and cancer. Although the correlations between abnormal centrosomes and chromosomal instability (CIN) and between CIN and carcinogenesis are well established, I haven't seen any suggestions in the literature that these correlations are due to abnormal centrioles and excessive PEF."

"I agree that CIN leads to various DNA defects that play a role in carcinogenesis. Other investigators have noted that there is no consistent pattern in such DNA defects (i.e., they vary from one type of cancer to another, and sometimes from one tumor to another of the same type in a different individual). Those investigators did not conclude that DNA defects are irrelevant, but only that CIN is the common denominator in carcinogenesis. I agree. Cancer is a complex disease, and there are surely many factors at work at various stages of the disease. My hypothesis is not about the downstream DNA defects, which everyone agrees are involved in disease progression, but only about how centrosomes might cause the CIN that apparently underlies those defects."

".. many causes might contribute to centrosome defects. One of those might be DNA mutations.. but there might also be other causes that are independent of DNA. For example, centrosomes are known to be sensitive to all kinds of intra- and extracellular stimuli; some of those might be known carcinogens such as smoke and asbestos. TOPS does not preclude a role for DNA mutations, but I would argue that by rejecting a neo-Darwinism-inspired overemphasis on DNA TOPS encourages scientists to see mutations as just one factor in the larger context of the cell and organism."

"I might add that I am merely proposing a hypothesis. I am not arguing that I have disproved neo-Darwinism or shown that DNA-centered cancer research has no value. Even if the hypothesis turns out to be true, it will merely demonstrate the value of taking a different approach to solving a biomedical problem."

"The PEF may work in conjunction with microtubule-associated motor proteins ("chromokinesins"), with the PEF acting primarily to bias movement away from the poles. If the hypothesis is true, then in cells about to undergo malignant transformation the PEF will increase after the onset of anaphase (since the centriolar turbines will fail to shut down), and the force will increase to much more than 5g."

".. the work on which I rely (and which I cite in my paper) deals with chromosomal instability in general and translocations in particular, not with aneuploidy."

"Actually, centrosome studies originated before the rise of the current molecular paradigm, but it is true that they continue to be conducted within this paradigm. My point is that "the basic theoretical model of cancer as a disease of somatic cell genetics" has not lived up to its promise -- namely, to illuminate the cause of cancer in a clinically fruitful way. It seems to me that a new approach is warranted. I'm betting on a different approach. Only time and further research will show [if] is successful."

"The scientific validity of ID depends on empirical findings and the logic of the design inference. In my opinion, there is already enough evidence to warrant the conclusions that,

(a) some features of the world are designed, and

(b) Darwinian evolution is false."

"The truth of ID does not depend on its scientific fruitfulness, and nowhere do I claim that my hypothesis bears on the truth of ID or the falsity of Darwinism. All I maintain is that my hypothesis (and others currently being generated within an ID framework) may help to demonstrate the fruitfulness of ID in guiding scientific research."

"My hypothesis proposes two forms of angular acceleration. The first involves the acceleration of the centriole pair inside the centrosome. When the Archimedes' screws first start rotating at the beginning of prometaphase the angular velocity of the centriole pair is zero. With the turbines generating a constant torque, the pair's revolutions would accelerate at a rate of approximately 10 Hz/sec, so that after twenty minutes their angular velocity would be of the order of 10 kHz. Viscosity effects would cause the fluid inside the centrosome to revolve with the pair (assuming the absence of friction due to nanobubbles on the inner walls)."

"The second form of angular acceleration would occur in the spindle, which would wobble due to the eccentricity of the revolutions of the centriole pair. This angular acceleration -- the centrifugal-like polar ejection force -- would be immediately transmitted to all objects in the spindle by microtubules."

"The vortexer analogy might help here. Some vortexers have a variable speed control, so one can start from zero and slowly increase the speed of the wobble; this is the first form of angular acceleration. The contents of a test tube inserted into the cup of the vortexer experience an angular acceleration (i.e., a centrifugal-like force) that forces the contents to climb up the inside of the tube; this is the second form of angular acceleration."


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Wednesday, October 19, 2005 12:42:00 PM  
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Friday, October 21, 2005 5:10:00 PM  
Anonymous Brian said...

I just thought I should point out that these following statements are entirely false:

"Recent research shows that "junk DNA" does, indeed, have previously unsuspected functions .. its results came as a complete surprise to people trying to ask Darwinian research questions."

"The fact that "junk DNA" is not junk has emerged not because of evolutionary theory but in spite of it."

...because the existence of a functionality for non-coding and other non-transcribed regions of the genome is explicitly predicted by natural selection. The metabolic costs of replication of vast amounts of useless DNA would impart a significant selective disadvantage compared with individuals with less of a metabolic load. Dilution of vital loci in a sea of "useless" DNA may reduce the probability of mutation due to environmental mutagens (think: radiation), or even systematically protect transcribed regions within a chromosomal superstructure of selectively-neutral DNA.

Wednesday, October 18, 2006 4:31:00 PM  

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