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In What Sense Design?
Biochemistry, Metabolism, & Life’s Origin
Stephen M. Contakes
Agenda
1. What’s the Big Deal?
2. Mainstream Science’s Explanation for Life
3. Intelligent Design’s Evaluation of the Data
4. Metabolism
5. A Suggested Way Forward
Part 1
What’s the Big Deal?
“Can you believe in God and Evolution?”:
“…you cannot coherently affirm the Christian-truth claim
and the dominant model of evolutionary theory at the
same time. … Evangelicals must absolutely affirm the
special creation of humans in God's image, with no
physical evolution from any nonhuman species.”
Albert Mohler, President,
Southern Baptist Theological Seminary*
Time, August 15, 2005.
We no longer have to resort to superstition when faced
with the deep problems: Is there a meaning to life? What
are we for? What is man? After posing the last of these
questions, the eminent zoologist G. G. Simpson put it thus: ‘The
point I now want to make is that all attempts to answer that
question before 1859 are worthless and that we will be
better off if we ignore them completely.’
Richard Dawkins, The Selfish Gene
Making Pronouncements
“[evolution] has not published and so it should perish.”
Michael Behe, Biochemist and Intelligent Design Proponent
in Darwin’s Black Box, 1995
“…you cannot coherently affirm the Christian-truth claim and the
dominant model of evolutionary theory at the same time. … Evangelicals
must absolutely affirm the special creation of humans in God's image,
with no physical evolution from any nonhuman species.”
Albert Mohler, President, Southern Baptist Theological Seminary*
*Quoted in Time, August 15, 2005.
Making Pronouncements
“a
delusive and arbitrary hypothesis tending towards
infidelity.”
“…false, and entirely contrary to the Holy Scripture.”
Making Pronouncements
Can Sometimes Make Us Look Foolish
“John Owen and John Wesley … rejected it as
a delusive and arbitrary hypothesis tending towards
infidelity.”
Quoted in Schaff, Philip History of the Christian Church, vol. 8:
the Swiss Reformation, 1882.
“…false, and entirely contrary to the Holy Scripture.”
Pope Paul V, 1616
These statements refer to the “Theory” that
the Earth revolves around the Sun
Can the Biblical creation accounts be
interpreted in harmony with evolution?
Yes.
Interpretations of Genesis 1 & 2 that are consistent with
naturalistic theories for Life’s origin do exist…
… although they may not accord with the dominant
understanding of these passages in Church history.
But,
Should the Biblical creation accounts be interpreted in
harmony with evolution?
Part 2
What is it we’re concerned about?
Mainstream Science’s Explanation
for Life
How did modern life arise? Scientific Questions
1. How did living systems arise from nonliving matter?
2. How did modern life forms come into existence?
How did modern life arise? Science’s Model
1. Chemical evolution
How did simple molecules
become biomolecules?
2. Self-Organization
How were the biomolecules
organized into a living system?
3. Biological evolution
How did living systems attain
their present form?
Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.
How did modern life arise? Science’s Answers
1. Chemical evolution
Don’t really know but have a
few ideas
2. Self-Organization
Don’t really know but have a
few ideas
3. Biological evolution
Evolutionary theory
Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.
What is Evolution?
Types of Evolution
“Microevolution”
Changes within a species – easily observed & reproducible
“Macroevolution”
divergence of two species from a common ancestor – not observed directly
Original Darwinian view:
Natural selection working on variation
Explains diversity of species, extinction, etc.. in a rough way
No convincing explanation of the underlying mechanism
Modification by Classical Genetics
Selection of genes is the underlying mechanism
Seen as changes in allelic frequencies between generations
Macroevolution/genes arise through chance mutations
Darwin’s Theory has Explanatory Power
Artificial Selection had already
been observed in the breeding
of animals
Natural selection applied this principle
to the distribution of species in
different environments
The figure at left is taken from www.evolution.berkeley.edu; that at right from http://focus.hms.harvard.edu/2006/090106/genetics.shtml
Evolutionary Theory and Common Ancestry
Key Idea
All life arose from a common ancestor
LUCA
Last Universal Common Ancestor
A “tree of life” can be constructed
showing how life arose
Notes
Species present when divergence
occurred are called common
ancestors
A common ancestor isn’t strictly
necessary for “macroevolution” to be
true
LUCA
Figure is taken from Voet, D.; Voet, J. G. Biochemistry ,
3rd
ed., Wiley, 2004.
Biochemistry & Molecular Biology Expand the Picture
Molecular Biology
Biochemistry
Genes are DNA sequences that
encode for functional molecules
i.e. molecules encode information
behind life
Most organisms are similar at the
molecular level
organism
organ
tissues
molecules
molecular
assemblies
Figures are taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.
cells
sub-cellular
organelles
Molecular Evolution
Protein and gene sequences contain embedded
information about evolutionary history
Assumptions:
Organisms evolved from common ancestors by altering
those ancestor’s protein and gene sequences.
Key idea:
Look at the sequence of the same protein from different species. The
number and location of differences relates to how long ago the two
species diverged from a common ancestor.
e.g. comparison of Myoglobin and the Hemoglobin a chain:
Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.
Differences Accumulate over time
The # of differences between
sequences increases linearly with
“time since divergence” from the
fossil record
Most differences don’t matter
i.e. don’t affect molecular function
Probably evolutionary accidents
# of differences per 100 amino acids
What does Molecular Evolution Tell Us?
Millions of years since divergence
(estimated from the fossil record)
Selecting out the bad occurs more often than selecting for the good
If your molecules don’t work you die, if they work better, you have a
slightly greater chance of reproducing
You can only get new function if you first copy the gene
This lets you keep the old design while you tinker with a new one
Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004 and is based on
Dickerson, R. E. The structures of cytochrome c and their rates of molecular evolution. J Mol Evol. 1971;1(1):26–45.
For more information see: Kimura, M; Tomoko Ohta, T. Proc Natl Acad Sci U S A. 1974 July; 71(7): 2848–2852.
Gene Duplication is Believed to be A Major
Mechanism for Molecular Evolution
The figure is taken from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002.
Molecular Evolution and Genome Sequencing
Support Gene Duplication
Taken from Cornish-Bowden, A. The Pursuit of Perfection: Biochemical Aspects of Evolution, Oxford, 2004.
Part 3
Intelligent Design’s Evaluation of the
Biochemical Data
Intelligent Design (ID):
“the Biochemical Challenge to Evolution”?
"If it could be demonstrated that any complex organ
existed, which could not possibly have been formed
by numerous, successive, slight modifications, my
theory would absolutely break down. But I can find
out no such case.”
Charles Darwin, The Origin of Species
Intelligent Design (ID):
“The Biochemical Challenge to Evolution”?
Irreducible Complexity = Designer
• Numerous cellular components are irreducibly complex
i.e. loss or malfunction of one component leads to loss of
function
• Consequently, they couldn’t have arisen by adaption
• So life must have been designed by a designer
The image at lower left is from Voet, D; Voet, J.; Biochemistry,3rd ed., Wiley, 2004.
Examples of “Irreducibly Complex” Systems
Bacterial Flagella
The Blood-Clotting Cascade
Images are from Voet, D; Voet, J.; Biochemistry,3rd ed., Wiley, 2004 and Voet, D; Voet, J.; & Pratt Fundamentals of Biochemistry, Wiley, 2004.
How did modern life arise? ID’s Answers
1. Chemical evolution
• No reasonable naturalistic
explanation
• “Best explanation” a designer
2. Self-Organization
• No reasonable naturalistic
explanation
• “Best explanation” a designer
3. Biological evolution
• Microevolution is OK
• Evolution hasn’t really
explained the origin of cells
and higher-level structures
• “Best explanation” a designer
Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.
Is ID Science?
What is science?
How Science works today: Methodological Naturalism
Philosophical Naturalism/Scientism
Only the physical world exists and everything can be explained in terms
of naturalistic explanations. God does not exist.
Methodological Naturalism
Science advances by looking for natural causes to explain phenomena.
The supernatural cannot be invoked as an explanation.
Science, fundamentally, is a game. It is a game with one overriding and
defining rule. Rule No. 1: Let us see how far and to what extent we can
explain the behavior of the physical and material universe in terms of
purely physical and material causes, without invoking the supernatural.
Dickerson, R. E. Perspectives on Science and Faith, 1992, 44,137.
What is Science? Who should decide?
The final point I want to make about Richard Dickerson’s argument is
that although he certainly didn’t intend it, it is a prescription for timidity.
It tries to restrict science to more of the same, disallowing a
fundamentally different explanation. It tries to place reality in a tiny
box, but the universe will not be placed in a box...
Behe, M. Darwins Black Box, Free Press, 1996.
Science, fundamentally, is a game. It is a game with one overriding and
defining rule. Rule No. 1: Let us see how far and to what extent we can
explain the behavior of the physical and material universe in terms of
purely physical and material causes, without invoking the supernatural.
Dickerson, R. E. Perspectives on Science and Faith, 1992, 44,137.
Is the Flagellum Irreducibly Complex?
Bacterial Flagellum
Type III Secretory Pathway
Key Idea:
The type III secretory pathway looks like a flagella without the filament
It is a plausible evolutionary precursor for the flagellum
ID response:
But it doesn’t work as a flagellum
It doesn’t fully explain the evolution of the flagellum
Images reproduced from Dembski, W.; Ruse, M. Debating Design, Oxford, 2004.
Part 4
Metabolism & ID
Metabolism: the Ultimate in Irreducible Complexity
Metabolism
Sum of all chemical reactions an
organism uses to:
• obtain & use energy
• grow
• sustain itself
• reproduce
Simplified Diagram of the Metabolic
Pathways in a Typical Cell →
All the reactions are
interconnected!!!
i.e. they depend on one another
The figure is taken from Voet, Voet, Pratt Fundamentals of
Biochemistry 2nd ed., Wiley, 2004.
Metabolism Made Simple
Catabolism
Example – Aerobic metabolism of glucose
• Fuel is “burned” to make energy:
Food & energy store oxidation
gives electrons
+
Reduction of an electron
acceptor to give energy
Anabolism
• Energy is used to make biomolecules:
Use electrons and energy from
catabolism to make
biomolecules
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O
C6H12O6 + 3 O2 →
3 ATP + 6 CO2 + 12 e+
12 e- + 3 O2 + 12 H+ →
6 H2O + ~30 ATP
Metabolism Made Slightly Less Simple
Food &
energy stores
ATP (energy) and
NADH (electrons)
Acetyl-CoA
NADH (electrons)
and GTP (energy)
CO2
NADH
(electrons)
O2
H 2O
The figure is adapted from Voet, Voet, Pratt Fundamentals of Biochemistry 2nd ed., Wiley, 2004.
Is the Citric Acid Cycle “Irreducibly Complex”?
Modern Aerobic Metabolism
glucose
Glycolysis
Glucose → 2 pyruvate
pyruvate
Acetyl-CoA Synthesis
pyruvate → Acetyl-CoA + CO2
Acetyl-CoA
Citric Acid
Cycle
CO2
CO2
Citric Acid
Cycle Result: Acetyl group → 2 CO2
Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002 & Voet, Voet, Pratt Fundamentals of Biochemistry, 2nd ed. Wiley, 2004.
Is the Citric Acid Cycle “Irreducibly Complex”?
Modern Aerobic Metabolism
glucose
Glycolysis
Glucose → 2 pyruvate
Many “Ancient” Prokaryotes only
have part of the Citric Acid Cycle
The “reductive branch” is run in
reverse to recover electrons
from fermentations
pyruvate
Acetyl-CoA Synthesis
pyruvate → Acetyl-CoA + CO2
Acetyl-CoA
Citric Acid
Cycle
CO2
CO2
Citric Acid
Cycle Result: Acetyl group → 2 CO2
Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002 & Voet, Voet, Pratt Fundamentals of Biochemistry, 2nd ed. Wiley, 2004.
Is the Citric Acid Cycle “Irreducibly Complex”?
Modern Aerobic Metabolism
glucose
Glycolysis
Glucose → 2 pyruvate
Many prokaryotes only have part
of the Citric Acid Cycle
and/or the “oxidative branch” is
run forward in some modern
prokaryotes grown anaerobically
pyruvate
Acetyl-CoA Synthesis
pyruvate → Acetyl-CoA + CO2
Acetyl-CoA
Citric Acid
Cycle
CO2
CO2
Citric Acid
Cycle Result: Acetyl group → 2 CO2
Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002 & Voet, Voet, Pratt Fundamentals of Biochemistry, 2nd ed. Wiley, 2004.
Is the Citric Acid Cycle “Irreducibly Complex”?
Modern Aerobic Metabolism
glucose
A Reverse Citric Acid Cycle could
have been used to “fix” carbon
Glycolysis
Glucose → 2 pyruvate
Some deeply-rooted Archea
actually run the cycle in reverse
pyruvate
Acetyl-CoA Synthesis
pyruvate → Acetyl-CoA + CO2
Biosynthesis
Acetyl-CoA
Acetyl-CoA
Citric Acid
Cycle
CO2
Reversed
Citric Acid
Cycle
CO2
CO2
Citric Acid
Cycle Result: Acetyl group → 2 CO2
CO2
2 CO2 → Acetyl group
Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002.
Part 5
A Suggested Way Forward ?
Possible Implications for an ID-based Faith
Short-term
No real effect or a slight loss of credibility with most scientists
Danger of subjugating Christianity to a particular science-based worldview
Possible long-term effects
Nothing – if no credible evolutionary pathways will be discovered
ID’s “god of the gaps” will shrink if credible evolutionary pathways are
discovered
Possible loss of faith if “irreducible complexity” and ID collapse due to the
discovery of highly-credible evolutionary pathways
Possible Implications for Accepting Evolution
Short-term
No real effect/loss of credibility with some Christians
Danger of subjugating our faith to a particular science-based worldview
Must face implications of evolution for our understanding of God & the
nature of Biblical revelation
Possible long-term effects
You will have to rethink your theology if future work eliminates evolution as
a scientific possibility
Nothing - if credible evolutionary pathways are discovered
Lessons from History
Natural Theology & William Paley’s Watch
… if the different parts had been differently shaped from what
they are, of a different size from what they are, or placed
after any other manner or in any other order than that in
which they are placed, either no motion at all would have
been carried on in the machine, or none which would have
answered the use that is now served by it.
William Paley, Natural Theology, 1800
Natural Theology at the Bar of History
“…whether natural theology, by claiming so much authority from science, might
not have dug its own grave…had Christian apologists not placed too great a
burden on arguments from design? … In fact, it would be a great mistake to
imagine that when the kind of phsico-theology we have been considering finally
collapsed, it came as a shock and embarrassment to every sector of the
Christian church. The vicissitudes of a science-based natural theology were
arousing anxieties in Britain from the earlier years of the nineteenth century.”
John Hedley Brooke*
*in Science and Religion: Some Historical Perspectives, Cambridge, 1991.
Perspectives to Consider
One Scientist’s:
Philosophically sophisticated people know that a “scientific” attack upon
religious belief is usually no less faulty than a defense of it. Scientists do not
speak on religion from a privileged position except insofar as those with a
predilection for the Argument from Design have better opportunities than
laymen to see the grandeur of the natural order of things, whatever they may
make of it.
P. B. Medawar, Advice to a Young Scientist
One Theologian’s:
In matters that are so obscure and far beyond our vision, we find in Holy
Scripture passages than can be interpreted in very different ways without
prejudice to the faith we have received. In such cases we should not rush in
headlong and so firmly take our stand on one side that, if further progress in
the search for truth justly undermines our position, we too fall with it.
Augustine of Hippo, On the Literal Meaning of Genesis*
*quoted by Francis Collins in The Language of God.
Intelligent Design or “Evolution”?
We should consider our answer with carefulness, humility,
& intellectual integrity
For we know in part and we prophesy in part, but when the perfect comes,
the partial will pass away. … For now we see in a mirror dimly, but then
face to face. Now I know if part; then I shall know fully, even as I have been
fully known.
Paul the Apostle, 1 Cor 13:9-10,12
*quoted in Williams, R.J.P.; daSilva J.J.R.F. The Natural Selection of the Chemical Elements, Oxford: 1996.
Acknowledgements
Bioc 380/381 Students, Fall 2006 – Spring 2007
Prof. Josh Morris, Azusa Pacific University
Prof. Sarah Richart, Azusa Pacific University