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How specific arguments defeat general dogmas: lack of parsimony in molecular biology Vlasta Sikimi c University of Belgrade December 2, 2016 Vlasta Sikimi c Argumentation in molecular biology December 2, 2016 1 / 21 Motivation How

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How specific arguments defeat general dogmas: lack of parsimony in molecular biology

Vlasta Sikimi´ c

University of Belgrade

December 2, 2016

Vlasta Sikimi´ c Argumentation in molecular biology December 2, 2016 1 / 21

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Motivation

How do you scratch your head?

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Motivation

Maximizing scientific knowledge as a whole. Optimal distribution of resources. Bigger picture – How do breakthrough results occur?

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Law of parsimony – Ockham’s Razor

Lex parsimoniae: other things being equal, we should prefer simpler theories to less simple ones. Kant:“Rudiments or principles must not be unnecessarily multiplied” (Critique of Pure Reason). Newton:“Nature is pleased with simplicity, and affects not the pomp

f superfluous causes” (Principia Mathematica).

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Ockham’s Razor in philosophy of science

Possible definition: Efficient method for finding the true theory, even if the truth is complex (K. Kelly 2004, 2007). Connections with induction: only hypothetical outcomes can be justifiably considered in the inductive analysis.

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Key questions

What is Ockham’s Razor in argumentation theory? How to optimize scientific argumentation?

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Choices

A case study approach; Molecular biology (a field-specific approach); Significant non-parsimonious results.

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Data-dirven and field-specific approach

Benefits of a case study approach: it is context dependent; it has a clear reach; and a straightforward application.

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Choices: Molecular biology

Dynamic argumentative flow in the field of molecular biology (versus e.g. contemporary experimental physics).

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Choices: Specific cases

Modern dilemmas; Nobel Prize winning research: Stanley B. Prusiner Thomas R. Cech

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Dogmas

D1: All infectious diseases are caused by an organism. (Koch’s postulate) D2: DNA encodes genetic material, RNA transmits it, proteins have a catalytic function. Summary: These are simple and universal explanations of the phenomena.

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Argumentation in molecular biology

Assumptions: Experimental results are considered to be truthful (unless they are deliberately faked) they defeat a hypothesis in the strong sense –they disprove it. Only hypotheses can contradict each other, i.e. attack each other. We only consider correct inferences.

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Argumentation example

R1

disproves

D1 ∧ H1

R1: Scrapie agent does not need to have intact nucleic acid. D1: All infectious diseases are caused by an organism. H1: All organisms need to have intact nucleic acid.

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Argumentation comparison

Cases in which a disease is caused by an organism e.g. anthrax. H: Disease is caused by a specific organism, e.g. bacillus. R1: Organism found! correlation R2 ∧ R3: Organism has to be grown in a pure culture and able to infect subjects. causation R2 ∧ R3 H Koch’s postulates.

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Argumentation comparison

R1 D1 ∧ H1 R2 D1 ∧ H2

R2: Scrapie agent can be killed by protein destroying treatment X. D1: All infectious diseases are caused by an organism. H2: Treatment X destroys proteins.

R3 D1 ∧ H3

R3: Scrapie agent is as small as a protein. H3: No organism is as small as a protein.

R4 H4 ∧ H5

R4: PrP protein is also in healthy organisms. H4: Protein has only one fold (no special features). H5: PrP protein causes the disease.

Simple correlation!

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Argumentation comparison

R5 ∧ R6: Expressed protein causes the disease. causation Convincing argument for the biological community. R5 ∧ R6 H5 Finally, since D1 logically contradicts H5: R5 ∧ R6 D1

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Note

R7

disproves

H1

R7: At least one organism is very resistant against DNA destructive treatment.

R1

disproves

D1 ∧ H1

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Second analysis: RNA has a catalytic function

Experimental results were showing that there is no protein

involved. correlation

The lack of energy requirement in the reaction. correlation Purified RNA had the same behaviour. correlation Elimination of different factors in reactions. correlation Exact findings. causation

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Level of inspection and frequences

Mutation scenarios are typical examples of non-parsimonious behaviour in biology. Phylogenetics (subfield of evolutionary theory) uses maximum parsimony as an optimality criterion. Yet, there are exceptions. (Rossell´

-Mora and Amann, 2001)

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Conclusions and further research

Conclusions: It is necessary to invest also in non-parsimonious ideas. Even if non-parsimonious behaviours are more prominent in molecular biology then in other disciplines, such behaviours are exceptions. Argumentation analysis helps us to understand important scenarios in which the principle of Ockham’s Razor is violated. Questions: When is it reasonable to consider non-parsimonious explanations? How many argumentative steps is reasonable to require?

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References

Kelly, Kevin. 2004. Justification as Truth-Finding Efficiency: How Ockham’s Razor Works. Minds and Machines 14: 485-505. Kelly, Kevin. 2007. A New Solution to The Puzzle of Simplicity. Philosophy of Science 74 (Proceedings): 561-73. Kelly Kruger, Paula J. Grabowski, Arthur J. Zaug, Julie Sands, Daniel E. Gottschling and Thomas R. Cech. 1982. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell 31: 147-157. Ramon Rossell´

-Mora and Rudolf Amann. 2001. The species concept

for prokaryotes. FEMS Microbiology Reviews 25: 39-67. Stanley B. Prusiner. 1982. Novel Proteinaceous Infectious Particles Cause Scrapie. Science 216: 136-144.

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