Thursday, June 07, 2007

A Divine Materialism

I've been reading the articles for the Institute for the Study of Nature's Summer Seminar. Certainly one of the most provocative that I've read so far is "Protein Folds as Platonic Forms," a 2002 paper by New Zealanders Michael Denton, Craig Marshall, and Michael Legge.

The article begins with an historical overview: biologists before Darwin believed organic forms to be eternal givens of nature: "Form came first and function was viewed as a secondary and derived adaptive feature" (326).

In contrast, the Darwinians (ironically) adopted Paley's watch metaphor: the organism as a machine, i.e., contingent order imposed from without. While the creationists emphasized God's work in imposing order on matter, the Darwinists replaced the Divine Designer with chance mutation and natural selection.

It's difficult to imagine a proto-lifeform reproducing itself before the cell, so chance locked in by reproduction isn't plausible in the case of life's original coming-to-be (the progenitor of the first cell):

The only area of modern biology where a strong deterministic and naturalistic element is still evident is the ‘‘origin of life’’ with many researchers viewing life’s origin as an inevitable and determined end of planetary and cosmic evolution (Kenyon & Steinman, 1969; Lehninger, 1982; De Duve, 1991; Morowitz et al., 2000; Sowerby et al., 2001). (329-330)

The Denton group's project is to extend this determinism beyond the origin of life, to show that the forms of proteins are determined by the natural laws of physics and chemistry, and not by the Darwinian mechanism of random mutation and selection:

Here we argue that in another important area of modern biology, one related to the origin of life, that involves the evolution and origin of one of the most important classes of complex biological forms—the basic protein folds — the pre-Darwinian concept of organic forms as ‘‘built-in’’ intrinsic features of nature determined by natural law provides a more powerful explanatory framework than its selectionist successor.1 (330)

The data show that proteins folds come in only about 1000 different natural kinds. These forms are determined from within, not from outside by the contingent choice of an intelligence or natural selection. In other words, the folding motions of proteins are natural to their materials, not artificially or violently imposed.

So you can see where this is going, I'll cut to the "money quote" from further on in the paper:

For the lawful nature of the [protein] folds provides for the first time evidence that the laws of nature may not only be fine tuned to generate an environment fit for life (the stage) but may also be fine tuned to generate the organic forms (the actors) as well, in other words that the cosmos may be even more biocentric than is currently envisaged! (338)

In other words, matter is pre-determined to bring forth life; the living order of the universe was front-loaded.

More Details

There's a lot more in this paper to recommend it, much more than I can capture in a single post. Here's a great quotation: "Natural forms are robust, contingent artificial forms are fragile." (333) The authors contrast a polypeptide's natural gravitation to its energy minimum with the contigent order of a watch or a Lego construction. While a perturbed natural form settles back into its minimum like a marbel settles into the bottom of a bowl, a perturbed artificial form usually loses its function.

The authors also note that that protein forms have a degree of independence from what they're made of:

The fact that in many cases where the same fold is adapted to different functions, no trace of homology [sameness] can be detected in the amino acid sequences [that compose it], suggesting multiple separate discoveries of the same basic structure during the course of evolution, further reinforces the conclusion that the folds are a finite set of ahistoric physical forms. (332)

This manifests what Robert Laughlin calls "protection": that the behavior of macro-phenomenon is unaffected by its particular micro-dynamics.

A Telling Contrast

It's interesting to contrast this conclusion with the divided Intelligent Design approach of Guillermo Gonzalez and Jay Richards in The Privileged Planet. Gonzalez and Richards tried to show that while the universe is "fine-tuned for life and discovery," life's organization didn't arise by necessity. They are walking a fine line: on the one hand, they want to show how God created the world to be good for life, but on the other hand, they don't want life to be the natural outcome of creation: "for a pattern to reliably indicate design, it will need to be relatively independent of the event or structure in question" (299).

But why do they trouble to walk this line? A passage from the book explains their fear:

Objection 13: You haven't really challenged naturalism. You've just challenged the idea that nature doesn't exhibit purpose or design.

It's possible to be both a naturalist and to admit design in nature. In fact, in the ancient world, both Aristotelians and Stoics did just that. Perhaps, for instance, design is somehow an inextricable part of an eternal cosmos, like matter and energy. We can't conclusively rule this out. The problem in our modern setting is that this strategy would require an essentially pantheistic view of nature that most naturalists deny. A cosmos that includes design and purpose—as well as chance, matter, and natural law—is quite different from "nature" as most modern naturalists understand it.

So they're afraid of "pantheism." Notice that they don't and can't rule out what they call "pantheism"; they just say that it's not a concern in today's world. It's unfortunate that they're too busy responding to exigent concerns to look more deeply into the full truth of the matter.2 And of course, pantheism is basically what Carl Sagan's Cosmos advocates, albeit without an explicit belief in purpose or design3. Furthermore, why do they oppose design and purpose with natural law? Doesn't natural law express purpose? The second paragraph of the passage is a little better, but still goes astray:

Moreover, current Big Bang cosmology discourages the view that the cosmos is eternal, which is necessary if design is coextensive with matter, time, and natural law (note also that law is not iself a material entity, nor is it a causal agent). A causal agent that somehow transcends the cosmos is a much more natural explanation for the Big Bang and the resulting physical universe we know than are purely immanent patterns of design. But either is a better explanation than the currently popular view that the physical universe is all there is, was, or ever shall be [opening line of Sagan's Cosmos!], and that chance and impersonal necessity exclusively explain its existence. (329, emphasis added)

The first sentence about law not being a causal agent is excellent. The highlighted sentence, on the other hand, shows a profound ignorance of philosophy. The use of the word "natural" is wrong on a couple levels. First, nature is an immanent source of motion and rest. Second, they make it sound as if God were a natural agent, when the whole philosophical point of invoking God is that the Existence of everything requires a source in a Agent that derives its Being from nothing else—in other words, a cause so completely unlike the changing world we see because it doesn't receive its being or motion from outside itself. Of course they're using "natural" loosely to mean reasonable. They fail to realize that even if the universe is eternal and all of its order completely immanent, it still requires a God to explain that order, as well as the existence of the universe in general. Philosophically speaking, the God (of the philosophers, not necessarily of revelation) is the only explanation possible.

In sum, ID proponents are afraid of pantheism, though it's not clear that they even understand what it is well enough to distinguish it from natural law, or purpose and design for that matter.


Three different views discussed here can be separated by the source of order:
1. From chance (Darwinism)
2. From intenvention by an intelligent agent (ID)
3. From within (Denton, et al.)

As we've already seen, all three of these require an Intelligent Designer, one who truly transcends nature. The ID folks are afraid of attributing too much self-organization to nature because they are frightened of pantheism—as if God wouldn't have to be responsible for whatever order the universe has through whatever mechanism! Contrary to the ID claim, there is no opposition between intelligence and law; laws require a Lawgiver. Contrary to the Darwinist claim, "chance" operates according to a law, which also requires an intelligence.

As Francis Bacon wrote so wisely in one of his Essays, "A little philosophy inclineth man's mind to atheism, but depth in philosophy bringeth men's minds about to religion." It is only the philosophical ignorance of the Darwinists that allows them to claim that chance obviates the need for God. The irony is that the ID approach feeds off this philosophical ignorance that "inclineth man's mind to atheism."

The Darwinists deny that God is necessary to make the "watch" of creation (Hence Dawkins's blind watchmaker). The ID crowd repudiates the deniers, but in doing so, they've imbibed the atheistic materialists' rather diminutive definition of God: a god who doesn't so much create matter as manipulate already existent matter.

When it comes down to it, it's impossible to devise a scientific scenario that doesn't need a Creator (science can't say anything about Being in itself). Intelligent design says that the order in the universe that can't be attributed to chance or law should really be attributed to an Intelligent Designer (God). There's nothing wrong with this belief in itself, but by denying that God can work through chance or law it sections off an unnecessarily small territory for theism—a territory that actual experience of the world seems to be chipping away.

The work of Michael Denton and his collaborators shows that at least some of the order of living things is native to the matter that constitutes them. Science cannot speak to the ultimate source of this order, but natural philosophy tells us that the source cannot be natural, but what men call God.


1. I've omitted references from this and all subsequent quotations.

2. It is sad that an organization like Discovery Institute with such a noble purpose tends to take such short-sighted approaches.

3. There's actually a whole Wikipedia discussion on Sagan and pantheism.

Michael J. Denton, Craig J. Marshall and Michael Legge, "Protein Folds as Platonic Forms," Journal of Theoretical Biology 219 (2002), 325–342

Michael J. Denton, et al., "Physical law not natural selection as the major determinant of biological complexity in the subcellular realm," BioSystems 71 (2003), 297-303.

Guillermo Gonzalez and Jay W. Richards, The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery (Washington, DC: Regnery, 2004).

Note: Next week I'll be traveling. I don't know what my network access will be like, but I may be unable to post.


David M. Smith said...

As always; great piece MJ!

Jim Baxter said...

The Season of Generation-Choicemaker
Joel 3:14 kjv

The missing element in every human 'solution' is
an accurate definition of the creature.

In an effort to diminish the multiple and persistent
dangers and abuses which have characterized the
affairs of man in his every Age, and to assist in the
requisite search for human identity, it is essential to
perceive and specify that distinction which naturally
and most uniquely defines the human being. Because
definitions rule in the minds, behaviors, and institutions
of men, we can be confident that delineating and com-
municating that quality will assist the process of resolu-
tion and the courageous ascension to which man is
called. As Americans of the 21st Century, we are oblig-
ed and privileged to join our forebears and participate
in this continuing paradigm proclamation.

"WHAT IS MAN...?" God asks - and answers:
by James Fletcher Baxter (c) AD 2007

The way we define 'human' determines our view of self,
others, relationships, institutions, life, and future. Many
problems in human experience are the result of false
and inaccurate definitions of humankind premised
in man-made religions and humanistic philosophies.

Human knowledge is a fraction of the whole universe.
The balance is a vast void of human ignorance. Human
reason cannot fully function in such a void; thus, the
intellect can rise no higher than the criteria by which it
perceives and measures values.

Humanism makes man his own standard of measure.
However, as with all measuring systems, a standard
must be greater than the value measured. Based on
preponderant ignorance and an egocentric carnal
nature, humanism demotes reason to the simpleton
task of excuse-making in behalf of the rule of appe-
tites, desires, feelings, emotions, and glands.

Because man, hobbled in an ego-centric predicament,
cannot invent criteria greater than himself, the humanist
lacks a predictive capability. Without instinct or trans-
cendent criteria, humanism cannot evaluate options with
foresight and vision for progression and survival. Lack-
ing foresight, man is blind to potential consequence and
is unwittingly committed to mediocrity, collectivism,
averages, and regression - and worse. Humanism is an
unworthy worship.

The void of human ignorance can easily be filled with
a functional faith while not-so-patiently awaiting the
foot-dragging growth of human knowledge and behav-
ior. Faith, initiated by the Creator and revealed and
validated in His Word, the Bible, brings a transcend-
ent standard to man the choice-maker. Other philo-
sophies and religions are man-made, humanism, and
thereby lack what only the Bible has:

1.Transcendent Criteria and
2.Fulfilled Prophetic Validation.

The vision of faith in God and His Word is survival
equipment for today and the future. Only the Creator,
who made us in His own image, is qualified to define
us accurately.

Human is earth's Choicemaker. Psalm 25:12 He is by
nature and nature's God a creature of Choice - and of
Criteria. Psalm 119:30,173 His unique and definitive
characteristic is, and of Right ought to be, the natural
foundation of his environments, institutions, and re-
spectful relations to his fellow-man. Thus, he is orien-
ted to a Freedom whose roots are in the Order of the

At the sub-atomic level of the physical universe quantum
physics indicates a multifarious gap or division in the
causal chain; particles to which position cannot be
assigned at all times, systems that pass from one energy
state to another without manifestation in intermediate
states, entities without mass, fields whose substance is
as insubstantial as "a probability."

Only statistical conglomerates pay tribute to
deterministic forces. Singularities do not and are
therefore random, unpredictable, mutant, and in this
sense, uncaused. The finest contribution inanimate
reality is capable of making toward choice, without its
own selective agencies, is this continuing manifestation
of opportunity as the pre-condition to choice it defers
to the natural action of living forms.

Biological science affirms that each level of life,
single-cell to man himself, possesses attributes of
sensitivity, discrimination, and selectivity, and in
the exclusive and unique nature of each diversified
life form.

The survival and progression of life forms has all too
often been dependent upon the ever-present undeterminative
potential and appearance of one unique individual organism
within the whole spectrum of a given life-form. Only the
uniquely equipped individual organism is, like The Golden
Wedge of Ophir, capable of traversing the causal gap to
survival and progression. Mere reproductive determinacy
would have rendered life forms incapable of such potential.

Only a moving universe of opportunity plus choice enables
the present reality.

Each individual human being possesses a unique, highly
developed, and sensitive perception of variety. Thus
aware, man is endowed with a natural capability for enact-
ing internal mental and external physical selectivity.
Quantitative and qualitative choice-making thus lends
itself as the superior basis of an active intelligence.

Human is earth's Choicemaker. His title describes
his definitive and typifying characteristic. Recall
that his other features are but vehicles of experi-
ence intent on the development of perceptive
awareness and the following acts of decision and
choice. Note that the products of man cannot define
him for they are the fruit of the discerning choice-
making process and include the cognition of self,
the utility of experience, the development of value-
measuring systems and language, and the accultur-
ation of civilization.

The arts and the sciences of man, as with his habits,
customs, and traditions, are the creative harvest of
his perceptive and selective powers. Creativity, the
creative process, is a choice-making process. His
articles, constructs, and commodities, however
marvelous to behold, deserve neither awe nor idol-
atry, for man, not his contrivance, is earth's own
highest expression of the creative process.

Human is earth's Choicemaker. The sublime and
significant act of choosing is, itself, the Archimedean
fulcrum upon which man levers and redirects the
forces of cause and effect to an elected level of qual-
ity and diversity. Further, it orients him toward a
natural environmental opportunity, freedom, and
bestows earth's title, The Choicemaker, on his
singular and plural brow.

Deterministic systems, ideological symbols of abdication
by man from his natural role as earth's Choicemaker,
inevitably degenerate into collectivism; the negation of
singularity, they become a conglomerate plural-based
system of measuring human value. Blunting an awareness
of diversity, blurring alternatives, and limiting the
selective creative process, they are self-relegated to
a passive and circular regression.

Tampering with man's selective nature endangers his
survival for it would render him impotent and obsolete
by denying the tools of variety, individuality,
perception, criteria, selectivity, and progress.
Coercive attempts produce revulsion, for such acts
are contrary to an indeterminate nature and nature's
indeterminate off-spring, man the Choicemaker.

Until the oppressors discover that wisdom only just
begins with a respectful acknowledgment of The Creator,
The Creation, and The Choicemaker, they will be ever
learning but never coming to a knowledge of the truth.
The rejection of Creator-initiated standards relegates
the mind of man to its own primitive, empirical, and
delimited devices. It is thus that the human intellect
cannot ascend and function at any level higher than the
criteria by which it perceives and measures values.

Additionally, such rejection of transcendent criteria
self-denies man the vision and foresight essential to
decision-making for survival and progression. He is left,
instead, with the redundant wreckage of expensive hind-
sight, including human institutions characterized by
averages, mediocrity, and regression.

Humanism, mired in the circular and mundane egocentric
predicament, is ill-equipped to produce transcendent
criteria. Evidenced by those who do not perceive
superiority and thus find themselves beset by the shifting
winds of the carnal-ego; i.e., moods, feelings, desires,
appetites, etc., the mind becomes subordinate: a mere
device for excuse-making and rationalizing self-justifica-

The carnal-ego rejects criteria and self-discipline for such
instruments are tools of the mind and the attitude. The
appetites of the flesh have no need of standards for at the
point of contention standards are perceived as alien, re-
strictive, and inhibiting. Yet, the very survival of our
physical nature itself depends upon a maintained sover-
eignty of the mind and of the spirit.

It remained, therefore, to the initiative of a personal
and living Creator to traverse the human horizon and
fill the vast void of human ignorance with an intelli-
gent and definitive faith. Man is thus afforded the
prime tool of the intellect - a Transcendent Standard
by which he may measure values in experience, anticipate
results, and make enlightened and visionary choices.

Only the unique and superior God-man Person can deserved-
ly displace the ego-person from his predicament and free
the individual to measure values and choose in a more
excellent way. That sublime Person was indicated in the
words of the prophet Amos, "...said the Lord, Behold,
I will set a plumbline in the midst of my people Israel."
Y'shua Mashiyach Jesus said, "If I be lifted up I will
draw all men unto myself."

As long as some choose to abdicate their personal reality
and submit to the delusions of humanism, determinism, and
collectivism, just so long will they be subject and re-
acting only, to be tossed by every impulse emanating from
others. Those who abdicate such reality may, in perfect
justice, find themselves weighed in the balances of their
own choosing.

That human institution which is structured on the
principle, "...all men are endowed by their Creator with
...Liberty...," is a system with its roots in the natural
Order of the universe. The opponents of such a system are
necessarily engaged in a losing contest with nature and
nature's God. Biblical principles are still today the
foundation under Western Civilization and the American
way of life. To the advent of a new season we commend the
present generation and the "multitudes in the valley of

Let us proclaim it. Behold!
The Season of Generation-Choicemaker Joel 3:14 KJV

"I should think that if there is one thing that man has
learned about himself it is that he is a creature of
choice." Richard M. Weaver

"Man is a being capable of subduing his emotions and
impulses; he can rationalize his behavior. He arranges
his wishes into a scale, he chooses; in short, he acts.
What distinguishes man from beasts is precisely that he
adjusts his behavior deliberately." Ludwig von Mises

"To make any sense of the idea of morality, it must be
presumed that the human being is responsible for his
actions and responsibility cannot be understood apart
from the presumption of freedom of choice."
John Chamberlain

"The advocate of liberty believes that it is complementary
of the orderly laws of cause and effect, of probability
and of chance, of which man is not completely informed.
It is complementary of them because it rests in part upon
the faith that each individual is endowed by his Creator
with the power of individual choice."
Wendell J. Brown

"These examples demonstrate a basic truth -- that human
dignity is embodied in the free choice of individuals."
Condoleeza Rice

"Our Founding Fathers believed that we live in an ordered
universe. They believed themselves to be a part of the
universal order of things. Stated another way, they
believed in God. They believed that every man must find
his own place in a world where a place has been made for
him. They sought independence for their nation but, more
importantly, they sought freedom for individuals to think
and act for themselves. They established a republic
dedicated to one purpose above all others - the preserva-
tion of individual liberty..." Ralph W. Husted

"We have the gift of an inner liberty so far-reaching
that we can choose either to accept or reject the God
who gave it to us, and it would seem to follow that the
Author of a liberty so radical wills that we should be
equally free in our relationships with other men.
Spiritual liberty logically demands conditions of outer
and social freedom for its completion." Edmund A. Opitz

"Above all I see an ability to choose the better from the
worse that has made possible life's progress."
Charles Lindbergh

"Freedom is the Right to Choose, the Right to create for
oneself the alternatives of Choice. Without the possibil-
ity of Choice, and the exercise of Choice, a man is not
a man but a member, an instrument, a thing."
Thomas Jefferson

Q: "What is man that You are mindful of him, and the son
of man that You visit him?" Psalm 8:4
A: "I call heaven and earth as witnesses today against
you, that I have set before you life and death, blessing
and cursing; therefore choose life, that both you and
your descendants may live." Deuteronomy 30:19

Q: "Lord, what is man, that You take knowledge of him?
Or the son of man, that you are mindful of him?" Psalm
A: "And if it seems evil to you to serve the Lord, choose
for yourselves this day whom you will serve, whether the
gods which your fathers served that were on the other
side of the river, or the gods of the Amorites, in whose
land you dwell. But as for me and my house, we will
serve the Lord." Joshua 24:15

Q: "What is man, that he could be pure? And he who is
born of a woman, that he could be righteous?" Job 15:14
A: "Who is the man that fears the Lord? Him shall He
teach in the way he chooses." Psalm 25:12

Q: "What is man, that You should magnify him, that You
should set Your heart on him?" Job 7:17
A: "Do not envy the oppressor and choose none of his
ways." Proverbs 3:31

Q: "What is man that You are mindful of him, or the son
of man that You take care of him?" Hebrews 2:6
A: "I have chosen the way of truth; your judgments I have
laid before me." Psalm 119:30 "Let Your hand become my
help, for I have chosen Your precepts."Psalm 119:173

Genesis 3:3,6 Deuteronomy 11:26-28; 30:19 Job 5:23
Isaiah 7:14-15; 13:12; 61:1 Amos 7:8 Joel 3:14
Ecclesiastes 3:1-8


Sir Isaac Newton
The greatest scientist in human history
a Bible-Believing Christian
an authority on the Bible's Book of Daniel
committed to individual value
and individual liberty

Daniel 9:25-26 Habakkuk 2:2-3 selah

"What is man...?" Earth's Choicemaker Psalm 25:12

An old/new paradigma - Mr. Jefferson would agree!
(Alternative? There is no alternative.)

+ + +

"Man cannot make or invent or contrive principles. He
can only discover them and he ought to look through the
discovery to the Author." -- Thomas Paine 1797

"Got Criteria?" See Psalm 119:1-176

semper fidelis
Jim Baxter
WWII & Korean War

Teacher, 5th Grade - 30 Wonderful years !
vincit veritas

"When you come to a fork in the road, take it!"
- Yogi Berra