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 1What’s the Big Deal?

“Can you believe in God and Evolution?”:

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

“…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*

“[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

These statements refer to the “Theory” that

the Earth revolves around the Sun

“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

Making PronouncementsCan Sometimes Make Us Look Foolish

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.

Should the Biblical creation accounts be interpreted in harmony with evolution?

But,

Part 2What 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?

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?

How did modern life arise? Science’s Model

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

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

How did modern life arise? Science’s Answers

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

What is Evolution?

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

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

Types of Evolution

“Microevolution”Changes within a species – easily observed & reproducible

“Macroevolution”divergence of two species from a common ancestor – not observed directly

Darwin’s Theory has Explanatory Power

The figure at left is taken from www.evolution.berkeley.edu; that at right from http://focus.hms.harvard.edu/2006/090106/genetics.shtml

Artificial Selection had already been observed in the breeding of animals

Natural selection applied this principle to the distribution of species in different environments

Evolutionary Theory and Common AncestryKey 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

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

LUCA

Biochemistry & Molecular Biology Expand the Picture

Biochemistry

Most organisms are similar at the molecular level

Molecular Biology

Genes are DNA sequences that encode for functional molecules

i.e. molecules encode information behind life

Figures are taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

molecules

molecular assemblies

sub-cellularorganelles

cells

tissues

organorganism

Molecular EvolutionProtein and gene sequences contain embedded information about evolutionary history

e.g. comparison of Myoglobin and the Hemoglobin chain:

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.

Assumptions:Organisms evolved from common ancestors by altering those ancestor’s protein and gene sequences.

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004 and is based onDickerson, R. E. The structures of cytochrome c and their rates of molecular evolution. J Mol Evol. 1971;1(1):26–45.

Differences Accumulate over time

The # of differences between sequences increases linearly with “time since divergence” from the fossil record

Millions of years since divergence(estimated from the fossil record)

# of

diff

ere

nce

s pe

r 10

0 a

min

o a

cids

What does Molecular Evolution Tell Us?

Most differences don’t matter

i.e. don’t affect molecular function

Probably evolutionary accidents

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

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

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 3Intelligent 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

Images are from Voet, D; Voet, J.; Biochemistry,3rd ed., Wiley, 2004 and Voet, D; Voet, J.; & Pratt Fundamentals of Biochemistry, Wiley, 2004.

Bacterial Flagella

The Blood-Clotting Cascade

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

How did modern life arise? ID’s Answers

Figure is taken from Voet, D.; Voet, J. G. Biochemistry , 3rd ed., Wiley, 2004.

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.

How Science works today: Methodological Naturalism

Philosophical Naturalism/ScientismOnly the physical world exists and everything can be explained in terms of naturalistic explanations. God does not exist.

Methodological NaturalismScience advances by looking for natural causes to explain phenomena. The supernatural cannot be invoked as an explanation.

What is science?

Is ID Science?

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.

What is Science? Who should decide?

Is the Flagellum Irreducibly Complex?

Key Idea:

The type III secretory pathway looks like a flagella without the filament

It is a plausible evolutionary precursor for the flagellum

Bacterial Flagellum Type III Secretory Pathway

Images reproduced from Dembski, W.; Ruse, M. Debating Design, Oxford, 2004.

ID response:

But it doesn’t work as a flagellum

It doesn’t fully explain the evolution of the flagellum

Part 4

Metabolism & ID

Metabolism: the Ultimate in Irreducible Complexity

Simplified Diagram of the Metabolic Pathways in a Typical Cell →

Metabolism

Sum of all chemical reactions an organism uses to:

• obtain & use energy

• grow

• sustain itself

• reproduce

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

Food & energy store oxidation gives electrons

+

Reduction of an electron acceptor to give energy

Anabolism

Use electrons and energy from catabolism to make

biomolecules

Example – Aerobic metabolism of glucose

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

• Fuel is “burned” to make energy:

• Energy is used to make biomolecules:

Metabolism Made Slightly Less SimpleFood &

energy stores

Acetyl-CoA

CO2

ATP (energy) and NADH (electrons)

NADH (electrons) and GTP (energy)

O2

H2O

NADH (electrons)

The figure is adapted from Voet, Voet, Pratt Fundamentals of Biochemistry 2nd ed., Wiley, 2004.

Citric Acid Cycle

GlycolysisGlucose → 2 pyruvate

Citric Acid Cycle Result: Acetyl group → 2 CO2

Acetyl-CoA Synthesispyruvate → Acetyl-CoA + CO2

CO2

CO2

Acetyl-CoA

pyruvate

glucose

Modern Aerobic Metabolism

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”?

GlycolysisGlucose → 2 pyruvate

Citric Acid Cycle Result: Acetyl group → 2 CO2

Acetyl-CoA Synthesispyruvate → Acetyl-CoA + CO2

CO2

CO2

Acetyl-CoA

pyruvate

glucose

Modern Aerobic Metabolism Many “Ancient” Prokaryotes only have part of the Citric Acid Cycle

Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002 & Voet, Voet, Pratt Fundamentals of Biochemistry, 2nd ed. Wiley, 2004.

Citric Acid Cycle

The “reductive branch” is run in reverse to recover electrons from fermentations

Is the Citric Acid Cycle “Irreducibly Complex”?

GlycolysisGlucose → 2 pyruvate

Citric Acid Cycle Result: Acetyl group → 2 CO2

Acetyl-CoA Synthesispyruvate → Acetyl-CoA + CO2

CO2

CO2

Acetyl-CoA

pyruvate

glucose

Modern Aerobic Metabolism Many prokaryotes only have part of the Citric Acid Cycle

Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002 & Voet, Voet, Pratt Fundamentals of Biochemistry, 2nd ed. Wiley, 2004.

Citric Acid Cycle

and/or the “oxidative branch” is run forward in some modern prokaryotes grown anaerobically

Is the Citric Acid Cycle “Irreducibly Complex”?

Reversed Citric Acid

Cycle

2 CO2 → Acetyl group

CO2

Acetyl-CoA

CO2

Biosynthesis

Citric Acid Cycle

GlycolysisGlucose → 2 pyruvate

Citric Acid Cycle Result: Acetyl group → 2 CO2

Acetyl-CoA Synthesispyruvate → Acetyl-CoA + CO2

CO2

CO2

Acetyl-CoA

pyruvate

glucose

Modern Aerobic Metabolism A Reverse Citric Acid Cycle could have been used to “fix” carbon

Figures are adapted from Fenchel, T. Origin and Early Evolution of Life., Oxford, 2002.

Is the Citric Acid Cycle “Irreducibly Complex”?

Some deeply-rooted Archea actually run the cycle in reverse

Part 5A Suggested Way Forward ?

Possible Implications for an ID-based Faith

Short-termNo real effect or a slight loss of credibility with most scientists

Danger of subjugating Christianity to a particular science-based worldview

Possible long-term effectsNothing – 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-termNo 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 effectsYou will have to rethink your theology if future work eliminates evolution as a scientific possibility

Nothing - if credible evolutionary pathways are discovered

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

Lessons from History

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.

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 Scientist’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*

One Theologian’s:

*quoted by Francis Collins in The Language of God.

Perspectives to Consider

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.

Intelligent Design or “Evolution”?

Acknowledgements

Bioc 380/381 Students, Fall 2006 – Spring 2007

Prof. Josh Morris, Azusa Pacific University

Prof. Sarah Richart, Azusa Pacific University