DM Outline IV

My continuing effort to organize blog entries into an outline so readers can better connect the dots (a consilience of clues).

A. Detecting Design

1. Science and Design

a. Outline the common definitions of ‘subjective’ and ‘objective.’

b. Identify problems with common definitions and propose George Cooper’s definition of objective that which can be measured by all parties who should obtain the same result given an appropriate range of accuracy.

c. Draw upon the wisdom of one the great biologists, Jacques Monod, to explain why science cannot determine whether or not life was designed.

d. Demonstrate how archeology and forensics fail to give us reason to think that science can determine whether or not life was designed.

e. Explain how most proponents and critics of design are likely to think alike on one issue – they will find it uncomfortable to acknowledge that science cannot determine whether or not life was designed.

2. Since detecting design is not science, consider other ways to approach this issue, document how my methodology closely parallels that of SETI

a. Seth Shostak

b. Stephen Novella

c. Paul Davies

d. Summary of similarities

3. The relevance of the Face on Mars

a. Higher resolution analysis leads to evidence for design

b. Logic of design inference – couple analogy to discontinuity

4. Ways to Approach a Design Inference

a. A key essay that outlines the four ways a design inference can be approached from outside the realm of science.

b. Explain designer-centrism and outline its problems. Also, designer-centrism entails agnosticism about the question of design.

c. Relating evidence and suspicion in an investigation. A case study from science that serves as an important caveat showing accumulating evidence need not point toward the truth.

d. It is important to distinguish between design and its implementation (ties in to Criterion of Rationality below).

5. Respond to a scientist’s review of The Design Matrix.

6. The subjective element inherent in assessing a design inference means that we need to be cognizant of the subjective dynamics in ourselves and others.

a. Intellectual honesty

b. Critical thinking

c. Naive Realism

d. Disconfirmation bias

B. Front-Loading Evolution (The Criterion of Foresight)

1. Outline the four subtle predictions that follow from front-loading. 1) Evolution would demonstrate deep homology; 2) Evolution would exhibit PREPA (the present explains the past); 3) Evolution would be significantly driven by intrinsic, biotic features; 4) Front-loading would be linked to terraforming.

a. Evolution would be significantly driven by intrinsic, biotic features

i. Evolution Under Intrinsic Control

ii. Evolution Under Intrinsic Control 2

iii. Molecular convergence under intrinsic control

iv. RecA as evolution gene

v. Cybernetic evolution

b. Front-loading would be linked to terraforming

i. Oxygen and multicellular evolution

ii. The molecular ingredient for wood found in algae (also possible example of PREPA)

iii. The hypothesis of terraforming predicts aerobic respiration should be front-loaded. Evidence to suggest it was.

iv. Oxygen may be older than we thought.


i. Needless complexity – Monosiga brevicollis

ii. Needless complexity of eukaryotes

iii. Metazoa depend on a particular cellular architecture needless for life to exist.

d. Evolution would demonstrate deep homology

i. Old vs. New ways of looking at evolution

ii. The molecular ingredient for wood found in algae (also possible example of PREPA)

iii. A calcium toolkit in protozoa

iv. Why deep homology is something that best fits with front-loading

v. Front-loading nervous system (evidence from synaptic machinery and development). Further evidence includes: Neurotransmitter toolkit and the nervous system is an example of convergent evolution

vi. Front-loading epithelial tissue – many components of epithelial tissue are found in unicellular protozoa

vii. The tyrosine kinase toolkit in single-celled life forms

viii. The homeodomain toolkit – preadaptation

ix. The Placozoan genome contains much circuitry needed for complex metazoan development.

x. Why only front-loading needs deep homology.

2. Address common misunderstandings about front-loading.

a. “The original front-loaded state had all the information needed to build complex, multi-cellular organisms (including humans).”

b. “Front-loading assumes that life began with a super-cell that contained all the genes needed to build complex multicellular life, including humans beings.”

c. “Why front-load?”

d. Front-loaded genes should be originally functionless

3. An engineer begins to contemplate the possibility of front-loading.

4. Evo-devo supports front-loading.

5. I predicted we would find metazoan-specific information in protozoan genomes back in 2002.

C. The Criterion of Rationality

1. Evolution is a protein-dependent reality and this has subtle, but crucial implications.

2. Proteins and DNA are very similar in a conceptual manner.

3. Respiration and photosynthesis are similar in a conceptual manner.

4. Receptor Tyrosine Kinases

5. The Genetic Code

a. The genetic code channels cytosine deamination.

b. The genetic code is exceptional at buffering against deleterious mutations.

c. The stop codons of the genetic code are special.

d. Does it display the hallmark features (see below) of the blind watchmaker?

6. The hallmarks of the blind watchmaker (the designer-mimic)

a. It produces features that are “good enough.”

b. It produces kluges.

c. It prefers the “easy ones.”

7. “It’s evolving. It’s doing what we designed it to do

D. The Criterion of Analogy

1. Ten years later, the machine “metaphor” continues to hold up.

2. Molecular biology is indebted to engineering concepts.

E. The Criterion of Discontinuity

1. Miller’s spark discharge experiment generates lots of clutter.

2. Seeding vs. Spawning

a. Strategies to enhance the success of seeding.

3. Evolution of the bacterial flagellum.

F. Future Directions

1. Horizontal transfer, biased gene conversion, and superorganisms.

a. Horizontal transfer of genetic material

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