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Induction. Realm of. Psychology. Philosophy of ..... Philosophers of Science would ask: “Why do you ..... as juxtaposition” [a list] than in “(…) the world as.
Not Plausible!

Even less Plausible!!!

Not Plausible!

Even less Plausible!!!

Not Plausible!

Even less Plausible!!!

Even less Plausible!!! WANTED Judgment & Decision Theory Making Rational Decisions

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, and the Question of the Possibility of “Plausibility-Tests“ Lars Vogt, Uni Bonn

Outline

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, 2 Questions be addressed and the will Question of the Possibility of “Plausibility-Tests“ 1) What is Hypothesis Testing and

why is it important? • general background • function in science • distinguish 2 basic types of Hypothesis Testing

Lars Vogt, Uni Bonn

Outline

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, 2 Questions be addressed and the will Question of the Possibility of “Plausibility-Tests“ 1) What is Hypothesis Testing and

why is it important? • general background

Goodness-of-Fit Tests

• function in science

• distinguish 2 basic types of Hypothesis Testing

Lars Vogt, Uni Bonn

Outline

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, 2 Questions be addressed and the will Question of the Possibility of “Plausibility-Tests“ 1) What is Hypothesis Testing and

why is it important? • general background

Goodness-of-Fit Tests

• function in science

• distinguish 2 basic types of Hypothesis Testing

Popperian Tests

Lars Vogt, Uni Bonn

Outline

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, 2 Questions be addressed and the will Question of the Possibility of “Plausibility-Tests“ 1) What is Hypothesis Testing and

why is it important?

Lars Vogt, Uni Bonn

2) What are Plausibility Tests? • what could that be?

• difference to other two basic types? • specific function?

Outline

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, 2 Questions be addressed and the will Question of the Possibility of “Plausibility-Tests“ 1) What is Hypothesis Testing and

why is it important?

Lars Vogt, Uni Bonn

Cladogram Testing in 2) What are Plausibility Tests? Phylogenetics

• what could that be?

• difference to other two basic types? • specific function?

Introduction

Inventorying

We love to make Lists of all sorts.

Inventorying

We love to make Lists of all sorts.

Who, When, What, Where, How many ?

Inventorying

We love to make Lists of all sorts.

Who, When, What, Where, Lists come in various forms:

In written form…

How many ?

Inventorying

…as a painting…

Inventorying

Who, When, What, Where, How many ?

…as a painting…

Inventorying

…or as a Collection

of Things.

Inventorying

Inventorying

…or as a Collection

of Things.

Inventorying

Collections

Inventorying

Collections

Classifications

Inventorying

Initial Taxonomies

Followed rather pragmatic

and cognitive principles

An Essential Distinction

Science vs Metaphysics

Organizing Inventories

Science vs Metaphysics

Organizing Knowledge

Demarcating Science from Pseudo-Science & Metaphysics

Science vs Metaphysics

Metaphysical Taxonomy

Science vs Metaphysics

Scientific Explanatory Taxonomy

Science vs Metaphysics

Scientific Explanatory Taxonomy

What makes Science Science?

Epistemic Virtues

Epistemic Virtues

Ockham’s Razor (Parsimony) Minimize the amount of Entities necessary for explaining a given phenomenon

Especially: Keep the amount of unobservable Entities at an absolute Minimum

Epistemic Virtues

Objectivity e.g. international measurement units;

Epistemic Virtues

Objectivity e.g. international measurement units; controlled vocabularies for semantic transparency (ontologies);

Epistemic Virtues

Objectivity e.g. international measurement units; controlled vocabularies for semantic transparency (ontologies); imaging techniques;

Epistemic Virtues

Objectivity e.g. international measurement units; controlled vocabularies for semantic transparency (ontologies); imaging techniques; documentation for procedural transparency

Epistemic Virtues

Objectivity e.g. international measurement units; Reproducibility, controlled vocabularies for semantic transparency (ontologies); operational & semantic imaging techniques; Transparency, documentation for procedural Communicability transparency

Epistemic Virtues

Truth-to-Nature

Epistemic Virtues

Truth-to-Nature Correspondence empirically relevant & applicable

Epistemic Virtues

Truth-to-Nature Correspondence empirically relevant & applicable

Coherence formally and logically correct

Epistemic Virtues

Truth-to-Nature Correspondence empirically relevant/ Grounding & applicable Substantiation

Coherence formally and logically correct

Epistemic Virtues

Truth-to-Nature Correspondence empirically relevant/ Grounding & applicable Substantiation

Coherence formally and logically correct Justification

Epistemic Virtues

Truth-to-Nature Correspondence empirically relevant & applicable Substantiation Grounding Judgment &/ Decision

Theory

Coherence Makingand Rational formally logicallyDecisions correct Justification

Judgment & Decision Making in Science

The Scientific Method

The Scientific Method

a Question or Phenomenon that

requires Explanation

The Scientific Method

formulate or modify an Explanation

The Scientific Method

formulate or modify an Explanation

deduce

The Scientific Method

formulate or modify an Explanation

deduce

designed to test the Hypothesis

The Scientific Method

formulate or modify an Explanation

perform the Experiment

deduce

designed to test the Hypothesis

The Scientific Method

Hypothesis Testing

perform the Experiment

designed to test the Hypothesis

Hypothesis Testing an Instrument for Judging and Making Rational Decisions in Science

Hypothesis Testing

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data.

Hypothesis Testing

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data. In case auf Causal Explanations, testing occurs against predicted Effects:

Hypothesis Testing

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data. In case auf Causal Explanations, testing occurs against predicted Effects: either direct Effects ’direct Evidence’ or

Hypothesis Testing

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data. In case auf Causal Explanations, testing direct Evidence occurs against predicted Effects: either direct Effects ’direct Evidence’ or

Hypothesis Testing

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data. In case auf Causal Explanations, testing direct Evidence occurs against predicted Effects: either direct Effects ’direct Evidence’ or indirect Effects ’indirect Evidence’.

Hypothesis Testing indirect Evidence

Hypothesis Testing Testing against relevant Experience (Observations, Measurements), i.e. Data. In case auf Causal Explanations, testing occurs against predicted Effects: either direct Effects ’direct Evidence’ or indirect Effects ’indirect Evidence’.

Hypothesis Testing

Evaluating a Hypothesis after Testing either: 1) Quantitatively

Hypothesis Testing

Evaluating a Hypothesis after Testing either: 1) Quantitatively (degree of support)

Hypothesis Testing

Evaluating a Hypothesis after Testing either: 1) Quantitatively (degree of support)

or 2) Qualitatively

Hypothesis Testing

Evaluating a Hypothesis after Testing either: 1) Quantitatively (degree of support)

or 2) Qualitatively

(yes/no; true/false)

Hypothesis Testing

Evaluating a Hypothesis after Testing either: (degree of support) 1) & Quantitatively Model Evidence-Weighting-Scheme

or 2) Qualitatively

(yes/no; true/false)

Hypothesis Testing

Evaluating a Hypothesis after Testing either: (degree of support) 1) & Quantitatively Model Evidence-Weighting-Scheme

or (yes/no; true/false) 2) Qualitatively Rationale for Verification/Falsification

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical) Tests, measuring Support and aiming at Confirmation

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical) Tests, measuring Support and aiming at Confirmation • no verification (i.e. no “proof of truth”)

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical) Tests, measuring Support and aiming at Confirmation • no verification (i.e. no “proof of truth”)

• measure only varying degrees of support

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical) Tests, measuring Support and aiming at Confirmation • no verification (i.e. no “proof of truth”)

• measure only varying degrees of support • “the more data the better”

Hypothesis Testing

Essential Requirement for Goodness-ofFit Approaches To be able to evaluate the relevance and impact of supporting and contradicting data:

Hypothesis Testing

Essential Requirement for Goodness-ofFit Approaches To be able to evaluate the relevance and impact of supporting and contradicting data: A Rationale for quantifying / measuring Evidence or Degree of Goodness-of-Fit, i.e. a “Weighting Scheme”.

Hypothesis Testing

Problem with Models & Weighting Schemes Each Model provides its own Framework for Analyzing and Evaluating Data, i.e. for Judging and Deciding on Hypotheses.

Hypothesis Testing

Problem with Models & Weighting Schemes Each Model provides its own Framework for Analyzing and Evaluating Data, i.e. for Judging and Deciding on Hypotheses. In some cases, for a given scientific task/question, different Types of Data require different Models for their analysis.

Hypothesis Testing

Problem with Models & Weighting Schemes Each Model provides its own Framework for Analyzing and Evaluating Data, i.e. for Judging and Deciding on Hypotheses. In some cases, for a given scientific task/question, different Types of Data require different Models for their analysis. different Models = different Frameworks

Hypothesis Testing

Problem with Models & Weighting Schemes Each Model provides its own Framework for Analyzing and Evaluating Data, i.e. for Judging and Deciding on Hypotheses.

Different Frameworks are In some cases, for a given scientific often incommensurable task/question, different Types of Data require different Models for their analysis. different Models = different Frameworks

Hypothesis Testing

Problem with Models & Weighting Schemes Each Model provides its own Framework for Analyzing and Evaluating Data, i.e. for Judging andof Deciding on Hypotheses. Results different Tests

Different Frameworks are befor incomparable In somecan cases, a given scientific often incommensurable task/question, different Types of Data

except for congruent/incongruent require different Models for their analysis. different Models = different Frameworks

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical) Tests, measuring Support and aiming at Confirmation

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests empirical (statistical)Support Tests, measuring Measuring Support and aiming at Confirmation

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Aiming at

empirical (statistical) Tests, measuring Hypothesis Confirmation Support and aiming at Confirmation

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Empirically relevant & applicable Focused on empirical (statistical) Tests, measuring Substantiation / Grounding Support and aiming at Confirmation

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Empirically relevant & applicable Focused on empirical (statistical) Tests, measuring Substantiation / Grounding Support and aiming at Confirmation

2) Popperian Tests Deduction based empirical Tests, aiming at the Falsification of the Hypothesis

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Empirically relevant & applicable Focused on empirical (statistical) Tests, measuring Substantiation / Grounding Support and aiming at Confirmation

2) Popperian Tests Deduction based empirical Tests, aiming Rejecting Hypotheses at the Falsification of the Hypothesis

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Empirically relevant & applicable Focused on empirical (statistical) Tests, measuring Substantiation / Grounding Support and aiming at Confirmation & Logically correct 2) PopperianFormally Tests Focused on Deduction based empirical Tests, aiming Justification at the Falsification of the Hypothesis

Hypothesis Testing

Hypothesis Testing

1) Goodness-of-Fit Tests Alternative

empirical (statistical) Tests, measuring Support and aiming at Confirmation 3rd Approach

2) Popperian Tests

Deduction based empirical Tests, aiming toatHypothesis Testing? the Falsification of the Hypothesis

3) … “Plausibility” Tests

Hypothesis Testing in Phylogenetics

Testing Cladograms

Hypothesis Testing in Phylogenetics

Underlying Task Reconstruction of a specific Sequence of certain Types of Causal Events that are specified in a Model by using putative Traces as direct Causal Indices (i.e. direct Evidence) and their Evaluation according to the Model.

Hypothesis Testing in Phylogenetics

Approach Task/Goal: Reconstruct the actual sequence of Speciation and Transformation events that have caused the data, resulting in a tree-like Representation.

Hypothesis Testing in Phylogenetics

Approach Task/Goal: Reconstruct the actual sequence of Speciation and Transformation events that have caused the data, resulting in a tree-like Representation.

Hypothesis Testing in Phylogenetics

Approach Task/Goal: Reconstruct the actual sequence of Speciation and Transformation events that have caused the data, resulting in a tree-like Representation.

Data: Distribution Patterns of Similarity of inheritable Properties across representatives of different taxa (OTUs), communicated in the form of Character Matrices.

Hypothesis Testing in Phylogenetics

Approach Task/Goal: Reconstruct the actual sequence of Speciation and Transformation events that have caused the data, INTRINSIC resulting in a tree-like Representation.

inheritable Data: Distribution Patterns of Similarity of inheritable Properties across Properties representatives of different taxa (OTUs), communicated in the form of Character Matrices. i.e. Direct Evidence

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. The Model should: • put the data in a meaningful causal relation to the tree-like representation;

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. The Model should: • put the data in a meaningful causal relation to the tree-like representation; •

all implicit assumptions should be consistent with relevant theories of presumed underlying causal processes.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. The Model should: • put the data in a meaningful causal Simple Model: relation to the tree-like representation; Parsimony should be • all implicit assumptions consistent with relevant theories of presumed underlying causal processes.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. The Model should: More complex Model: • put the data in a meaningful causal relation to the tree-like representation; Likelihood / Bayes • all implicit assumptions should be with substitution model consistent with relevant theories of presumed underlying causal processes.

A Consequence of the Model

Hypothesis Testing in Phylogenetics

formulate or modify an Explanation

Classical through generalization, extrapolation, assuming causal mechanisms for observable correlations, approximation,…

Hypothesis Testing in Phylogenetics

theoretical Framework in Phylogenetics In Cladistic Analyses, already the Model defines :

Hypothesis Testing in Phylogenetics

theoretical Framework in Phylogenetics In Cladistic Analyses, already the Model defines : 1) the general type of hypothesis: tree-shaped

Hypothesis Testing in Phylogenetics

theoretical Framework in Phylogenetics In Cladistic Analyses, already the Model defines : 1) the general type of hypothesis: tree-shaped 2) a limited Hypothesis Space: Tree-Space.

Hypothesis Testing in Phylogenetics

theoretical Framework in Phylogenetics In Cladistic Analyses, already the Model defines : 1) the general type of hypothesis: tree-shaped 2) a limited Hypothesis Space: Tree-Space. Consequence: Set of possible Cladograms not inferred but depends on #OTUs and is given prior to analysis!

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map & Optimize Data for each Tree from Tree-Space using the Weighting Scheme.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map & Optimize Data for each Tree from Tree-Space using the Weighting Scheme. 3) Evaluate and Compare total Weight of Evidence of Data across all Trees.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map & Optimize Data for each Tree from Tree-Space using the character-related: Weighting Scheme. Weighting Scheme for 3) Evaluate and Compare total Weight Phylogenetic of EvidenceCharacters of Data across all Trees.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map & Optimize Data for each Tree from Tree-Space using e.g. the clade-related: character-related: Weighting Scheme. Weighting #Apomorphies, Scheme for 3) Evaluate and Compare total Weight Bootstraps Phylogenetic Values, of Evidence of Data across all Trees. Bremer Characters Support

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map & Optimize Data for each Tree from Tree-Space using e.g. the clade-related: character-related: Weightingtree-related: Scheme. e.g. Weighting #Apomorphies, Scheme for 3) Evaluate and Compare total Weight #Steps, CI, Lh Value Bootstraps Phylogenetic Values, of Evidence of Data across all Trees. Bremer Characters Support

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme.

Goodness-of-Fit

2) Map & Optimize Data for each Tree from Tree-Space using the Weighting Scheme.

Cladogram Testing 3) Evaluate and Compare total Weight of Evidence of Data across all Trees.

Hypothesis Testing in Phylogenetics

Approach 1) Develop a Model of Evolution that is relevant, including a Rationale for a Weighting Scheme. 2) Map &INTRINSIC Optimize Data for each Tree from Tree-Space using the Weighting Scheme.

TEST 3) Evaluate and Compare total Weight of Evidence of Data across all Trees.

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit Measures can be interpreted based on the underlying Model.

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit Measures can be interpreted based on the underlying Model. Measures for alternative Trees can be compared and provide a scientific Justification for the Choice of a presently best Explanation of the Data.

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit Measures can be interpreted based on the underlying Model. Measures for alternative Trees can be compared andBUT provide a scientific Justification for the Choice of a presently best Explanation of the Data.

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit They Generalize from a Measures beof interpreted based limitedcan Set Instances to on the underlying Model.

all Instances Measures for alternative Trees can be compared and provide a scientific Justification for the Choice of a presently best Explanation of the Data.

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit They Generalize from a Measures beof interpreted based limitedcan Set Instances to on the underlying Model.

all Instances Measures for alternative Trees can be compared and provide a scientific Justification for the Choice of a presently They infer from these best Explanation of the Data.

Instances a general Causal Regularity

Hypothesis Testing in Phylogenetics

Measures of Goodness-of-Fit They Generalize from a Measures beof interpreted based limitedcan Set Instances to on the underlying Model.

Criticized for being all Instances Measures for alternative Trees can be Inductivist

compared andBUT provide a scientific Justification for the Choice of a presently They infer from these best Explanation of the Data.

Instances a general Causal Regularity

Modes of Inference: Induction

Induction

Case

These beans are from this bag

Induction

Case

These beans are from this bag

Result These beans are white

Induction

Case

These beans are from this bag

Result These beans are white

.·. Rule

All the beans from this bag are white

Induction

Case

These beans are from this bag

Result These beans are white

.·. Rule

All the beans from this bag are white

Induction

Case

These beans are from this bag

Induction is synthetical: A finite Set of Observations is used for gaining new Result These beans are white Knowledge

.·. Rule

All the beans from this bag are white

Problem of Induction

Problem of Induction

Case

Result

.·. Rule

requires a Principle of Induction

Problem of Induction

Case

Result

.·. Rule

Substantiation / Grounding requires a Principle of Induction Justification

Problem of Induction

Case

Result

.·. Rule

Substantiation / Grounding requires a Principle of Induction Justification

Trilemma of Induction

Case

Principle of Induction • Circular Reasoning

Result

.·. Rule

Trilemma of Induction

Case

Principle of Induction • Circular Reasoning • Infinite Regression

Result

.·. Rule

Trilemma of Induction

Case

Principle of Induction • Circular Reasoning • Infinite Regression

Result • Dogmatism

.·. Rule

Trilemma of Induction

Case

Principle of Induction • Circular Reasoning • Infinite Regression

Result • Dogmatism

.·. Rule

Trilemma of Induction

Case

Problem of Induction Principle of Induction • Circular Reasoning • Infinite Regression

Result • Dogmatism

.·. Rule

David Hume (1711-1776)

Trilemma of Induction

Case

Problem of Induction Principle of Induction • Circular Reasoning

Result

• Infinitean Regression Is there • Dogmatism Alternative?

.·. Rule

David Hume (1711-1776)

Popper‘s Falsificationism

Sir Karl Raimund Popper (1902-1994)

Popper’s Approach

Deduction

Induction

Popper’s Approach

Deduction Deduction is analytical: No new Knowledge gained; Existing Knowledge is only Induction rephrased

Popper’s Approach

Deduction

Induction

Popper’s Approach

Deduction

Induction

Realm of Psychology

Popper’s Approach

Deduction

Induction

Philosophy of Science

Realm of Psychology

Asymmetry of Falsification vs Verification

Initial Idea Distinguishing “All-Sentences”

from “Some-Exist-Sentences”

Deduction - modus tollens

Hypothesis

All the beans from this bag are white

Deduction - modus tollens

Hypothesis

All the beans from this bag are white.

Prediction

All beans taken from this bag will be white.

Deduction - modus tollens

Hypothesis

All the beans from this bag are white.

Prediction

All beans taken from this bag will be white.

contradicting Observation

Some beans exist that are from this bag

that are NOT white.

Demarcation Criterion

In case the Observation is true, modus tollens proves that the Hypothesis is false.

The Hypothesis is thus, in principle,

falsifiable.

Demarcation Criterion

Science Knowledge

Metaphysics Opinion, Believe, Pseudo-Science

Demarcation Criterion

Science Knowledge

Deduction - modus tollens

Hypothesis

All the beans from this bag are white.

Prediction

All beans taken from this bag will be white.

contradicting Observation

Some beans exist that are from this bag

that are NOT white.

Deduction - modus tollens

Hypothesis

All the beans from this bag are white.

Very well suited for the so called EXPERIMENTAL SCIENCES, Prediction All beans taken from this bag will be white. that infer PREDICTIONS from contradicting Some beans exist that are from this bag UNIVERSAL CAUSAL LAWS. Observation that are NOT white.

The Scientific Method

formulate or modify an Explanation

deduce

Experimental

Sciences

perform the Experiment

design to Test the Hypothesis

Deduction - modus tollens

In Experimental Sciences

Theoretical Entity Electron

Deduction - modus tollens

In Experimental Sciences Theory Predicted Necessary Theoretical Entity Causal Effect Electron

emitting Light when changing to Orbit closer to Nucleus

Deduction - modus tollens

In Experimental Sciences Theory Predicted Necessary Theoretical Entity Causal Effect emitting Light when changing to Orbit closer to Nucleus

Electron

Electron in the Lab

Practice

Actual Observable/ Measurable Effect

Deduction - modus tollens

In Experimental Sciences Theory Predicted Necessary Theoretical Entity Causal Effect emitting Light when changing to Orbit closer to Nucleus

Electron

Electron in the Lab

Practice

Actual Observable/ Measurable Effect

Hypothesis Corroborated Observed/ Measured Effect

Predicted Necessary Causal Effect

Deduction - modus tollens

In Experimental Sciences Theory Predicted Necessary Theoretical Entity Causal Effect emitting Light when changing to Orbit closer to Nucleus

Electron

Electron in the Lab

Practice

Actual Observable/ Measurable Effect

Hypothesis Falsified Observed/ Measured Effect

Predicted Necessary Causal Effect

Deduction - modus tollens

In Experimental Sciences Theory Predicted Necessary Theoretical Entity Observation Causal Effect A single can be Electron

emitting Light when changing to Orbit closer to Nucleus

already sufficient, i.e. Practice

Electron in the Actual Observable/ qualitative decisive, for Lab Measurable Effect

Falsification Hypothesis Falsified Corroborated Observed/ Measured Effect

Predicted Necessary Causal Effect

FALSIFICATIONISM & PHYLOGENETICS

FALSIFICATIONISM & PHYLOGENETICS

Justification of the best Method of Classification

Justification of the best Method FALSIFICATIONISM & of Reconstructing Phylogeny PHYLOGENETICS

Falsification & Phylogenetics

In order to be scientific sensu Popper, a Phylogenetic Hypothesis must be capable of failing against experience.

Falsification & Phylogenetics

In order to be scientific sensu Popper, a Phylogenetic Hypothesis must be capable of

With NO INDUCTION involved !

failing against experience.

Falsification & Phylogenetics

In order to be scientific sensu Popper, a Phylogenetic Hypothesis must be capable of failing against experience.

In other words, the Hypothesis must be

FALSIFIABLE in principle.

Falsification & Phylogenetics

Are Cladograms falsifiable?

Falsification & Phylogenetics

Are Cladograms falsifiable?

How do we Test Cladograms in Phylogenetic Research Practice?

Falsification & Phylogenetics

Empirical Basis: Distribution Patterns of Similarity among inheritable Properties of Organisms.

Falsification & Phylogenetics

Empirical Basis: Distribution Patterns of Similarity among inheritable Properties of Organisms. What is the deductive Link between a

given Pattern and a specific Cladogram? Can a Cladogram deductively contradict any given Pattern?

Falsification & Phylogenetics

NO DEDUCTIVE CONTRADICTION Pattern NOT prohibited by this Cladogram!

Falsification & Phylogenetics

AGAIN: NO DEDUCTIVE CONTRADICTION Again: Pattern NOT prohibited by this Cladogram!

Falsification & Phylogenetics

Falsification & Phylogenetics

No deductive link between cladograms and the empirical basis used for their reconstruction

Falsification & Phylogenetics

Problem: The Background Knowledge Theory of Evolution provides more than one possible Explanation for an observed Pattern of Similarity of inheritable organismic Properties.

Falsification & Phylogenetics

Problem: The Background Knowledge Theory of Evolution provides more than one possible Apomorphy Explanation for an observed Pattern of

Homoplasy Similarity of inheritable organismic Properties.

Falsification & Phylogenetics

In Diagnostic Sciences

Theoretical Entity Cladogram/Monophylum

Falsification & Phylogenetics

In Diagnostic Sciences Theory

Theoretical Entity Cladogram/Monophylum

Predicted Necessary Causal Effect

Falsification & Phylogenetics

In Diagnostic Sciences Theory

Theoretical Entity Cladogram/Monophylum

“Retrodicted” Necessary Causal Effect

Falsification & Phylogenetics

In Diagnostic Sciences Theory

Theoretical Entity Cladogram/Monophylum

“Retrodicted” Necessary Causal Effect

Falsification & Phylogenetics

In Diagnostic Sciences Theory

Theoretical Entity Cladogram/Monophylum

Congruence Test

“Retrodicted” Necessary Causal Effect

Falsification & Phylogenetics

In Diagnostic Sciences Theory

Theoretical Entity Cladogram/Monophylum

Congruence Test

“Retrodicted” Necessary Causal Effect

“Falsifies” Sets of Apomorphy Hypothesis

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem: NO intrinsic heritable Property contradicts any given Cladogram/Monophylum.

NO Character can serve as potential Falsifier for any given Cladogram/

Monophylum.

Falsification & Phylogenetics

Problem:

Falsificationism NO intrinsic heritable Property contradicts not well suited for any givenDIAGNOSTIC Cladogram/Monophylum. SCIENCE, because they usually do not infer PREDICTIONS NO Character can serve as potential from Falsifier for any given Cladogram/ UNIVERSAL CAUSAL LAWS. Monophylum.

Falsification & Phylogenetics

Problem: EXPERIMENTAL SCIENCE NO intrinsic heritable =Property contradicts

“HARD SCIENCE” any given Cladogram/Monophylum. NO Character can serve as potential

DIAGNOSTIC SCIENCE Falsifier for any=given Cladogram/ “SOFT SCIENCE” Monophylum.

Conclusion

Vogt (2008) The unfalsifiability of cladograms and its consequences. Cladistics 24: 62-73.

Consequence* Science Knowledge

Metaphysics Opinion, Believe, Pseudo-Science

Consequence* Science Knowledge

* BUT: Falsificationism has been Criticized for several Reasons

Criticism

DUHEM-QUINE Thesis Every empirical Test requires some auxiliary assumptions, i.e. Background Knowledge.

Criticism

DUHEM-QUINE Thesis Every empirical Test requires some auxiliary assumptions, i.e. Background Knowledge.

All predictions rest on these assumptions.

Criticism

DUHEM-QUINE Thesis Every empirical Test requires some auxiliary assumptions, i.e. Background Knowledge.

All predictions rest on these assumptions. Thus, the consequences of a test also rest on these assumptions.

Criticism

Whereas the Set DUHEM-QUINE Thesis Every empirical Test requires some auxiliary {HYPOTHESIS,

BACKGROUND KNOWLEDGE, assumptions, i.e. Background Knowledge. OBSERVATIONS} All predictions rest on these assumptions.

can be falsified as a whole, no Thus, the consequences of a can test also single component of the set be in principle. restfalsified on these assumptions.

Criticism

Conclusion from DUHEM-QUINE Thesis Whereas a Hypothesis can be falsifiable in

principle, it cannot be actually falsified.

Criticism

Conclusion from DUHEM-QUINE Thesis Whereas a Hypothesis can be falsifiable in

principle, it cannot be actually falsified. Claiming true Falsification of a hypothesis commits the mistake of naïve strict

Falsificationism.

Back to Hypothesis Testing in Phylogenetics

Hypothesis Testing in Phylogenetics

So far…

Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Hypothesis Testing in Phylogenetics

So far…

Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Hypothesis Testing in Phylogenetics

So far…

Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Hypothesis Testing in Phylogenetics

So far…

Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Tests using other Sources of Data

Hypothesis Testing & Types of Data

Classifying Types of Data for Testing Cladograms based on Biology

Hypothesis Testing & Types of Data

Classifying Types of Data for Testing Cladograms based on Biology intrinsic heritable Properties

intrinsic Tests

Hypothesis Testing & Types of Data

Classifying Types of Data for Testing Cladograms based on Biology intrinsic heritable Properties

intrinsic Tests

extrinsic Features

extrinsic Tests

not inheritable

Hypothesis Testing & Types of Data

Classifying Types of Data for Testing Cladograms based on Biology intrinsic heritable Properties

intrinsic Tests

extrinsic extrinsic Features require a different ModelTests not inheritable

Hypothesis Testing & Types of Data

Classifying Types of Data for Testing Cladograms based on Biology intrinsic heritable Properties

intrinsic Tests

PLAUSIBILITY extrinsic extrinsic Features require a different ModelTests not inheritable

TEST ?

Hypothesis Testing in Phylogenetics

Plausibility Test Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Hypothesis Testing in Phylogenetics

Plausibility Test Type of Hypothesis

Type of Test

Cladogram/Monophylum

Goodness-of-Fit

intrinsic heritable

Popperian

intrinsic heritable

Plausibility

intrinsic heritable

Hypothesis Testing & Types of Data

Plausibility Test Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

intrinsic

extrinsic

Popperian

intrinsic

extrinsic

Hypothesis Testing & Types of Data

Extrinsic Features used for Testing Cladograms

Hypothesis Testing & Types of Data

Extrinsic Features used for Testing Cladograms • strata of fossil taxa / taxon age

Hypothesis Testing & Types of Data

Extrinsic Features used for Testing Cladograms • strata of fossil taxa / taxon age • geographical distribution

Hypothesis Testing & Types of Data

Extrinsic Features used for Testing Cladograms • strata of fossil taxa / taxon age • geographical distribution

• associates (i.e. parasites, symbionts)

Hypothesis Testing & Types of Data

Extrinsic Features used for Testing Cladograms • strata of fossil taxa / taxon age • geographical distribution

• associates (i.e. parasites, symbionts) • preferred habitat •…

Using STRATA DATA for Goodness-of-Fit Tests

Hypothesis Testing in Phylogenetics using Strata Data

Known Fossil Record

© Peter Schmid

© Ray Troll

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Hypothesis Testing in Phylogenetics using Strata Data

Known TheFossil Fossil Record Record confirms the Cladogram Hypothesis

© Peter Schmid

© Ray Troll

http://www.mediadesk.uzh.ch/articles/2010/Neue-Hominidenart/ Phylogeny.jpg

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Hypothesis Testing in Phylogenetics using Strata Data

Known Fossil Record BUT: Taxon Ages are not heritable, thus carry no Homology Information, thus cannot be Phylogenetic Characters Grandcolas et al. (2011) Mapping extrinsic traits such as extinction risks or modelled bioclimatic niches on phylogenies: does it make sense at all? Cladistics 27(2): 181-185.

© Peter Schmid

© Ray Troll

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http://www.earth-time.org/trollart.html

Hypothesis Testing in Phylogenetics using Strata Data

Known Fossil Record

Problem:

BUT: Taxon Ages are not heritable, No Rationale for thus carry no Homology Information, Quantifying Weight of Evidence thus cannot be Phylogenetic Characters Grandcolas et al. (2011) Mapping extrinsic traits such as extinction risks or modelled bioclimatic niches on phylogenies: does it make sense at all? Cladistics 27(2): 181-185.

© Peter Schmid

© Ray Troll

http://www.mediadesk.uzh.ch/articles/2010/Neue-Hominidenart/ Phylogeny.jpg

http://www.earth-time.org/trollart.html

Hypothesis Testing in Phylogenetics using Strata Data

Known Fossil Record

Problem:

BUT: TaxonBut Ages are not heritable, maybe a Candidate No Rationale for thus carry noforHomology Information, a Plausibility Test of Quantifying Weight of Evidence thus cannot beCladogram Phylogenetic Characters Hypotheses? Grandcolas et al. (2011) Mapping extrinsic traits such as extinction risks or modelled bioclimatic niches on phylogenies: does it make sense at all? Cladistics 27(2): 181-185.

© Peter Schmid

© Ray Troll

http://www.mediadesk.uzh.ch/articles/2010/Neue-Hominidenart/ Phylogeny.jpg

http://www.earth-time.org/trollart.html

Direct and indirect Data:

direct and indirect Tests ?

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process intrinsic heritable Properties

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process intrinsic heritable Properties

direct Evidence

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process intrinsic heritable Properties

direct Evidence

indirectly affected by the Causal Process

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process intrinsic heritable Properties

direct Evidence

indirectly affected by the Causal Process extrinsic Features not inheritable

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model direct Participants in the Causal Process intrinsic heritable Properties

direct Evidence

indirectly affected by the Causal Process extrinsic Features not inheritable

indirect Evidence

Direct & indirect Tests of Cladograms

Classifying Types of Data for Testing Cladograms based on the Causal Model indirect Evidence intrinsic heritable

Properties

extrinsic Features direct Evidence not inheritable

direct Evidence

indirect Evidence

Direct & indirect Tests of Cladograms

Direct & indirect Tests of Cladograms Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Direct & indirect Tests of Cladograms

Direct & indirect Tests of Cladograms Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Direct & indirect Tests of Cladograms

Direct & indirect Tests of Cladograms Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Using STRATA DATA for Popperian Tests

Hypothesis Testing in Phylogenetics using Strata Data

Assuming that…

Hypothesis Testing in Phylogenetics using Strata Data

Known Fossil Record Assuming that…

© Peter Schmid

© Ray Troll

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Hypothesis Testing in Phylogenetics using Strata Data

NEW Fossil Record Assuming that…

© Peter Schmid

© Ray Troll

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Hypothesis Testing in Phylogenetics using Strata Data

Known NEW IF the New Fossil Fossil Record Record were true, Assuming that…

the Cladogram would be Falsified

© Peter Schmid

© Ray Troll

http://www.mediadesk.uzh.ch/articles/2010/Neue-Hominidenart/ Phylogeny.jpg

http://www.earth-time.org/trollart.html

Hypothesis Testing in Phylogenetics using Strata Data

Known NEW IF the New Fossil Fossil Record Record were true,

“temporal order Assuming that… the Cladogram

would be Falsified carries information” Fisher (2008) Stratocladistics: Integrating temporal data in phylogenetic inference. Ann. Rev. Ecol. Syst. 39: 365-385.

© Peter Schmid

© Ray Troll

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Hypothesis Testing in Phylogenetics using Strata Data

Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Type of Hypothesis Type of Test

Cladogram/Monophylum Goodness-of-Fit

direct

indirect

Popperian

direct

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Contemporary

Type of Hypothesis

Type of Test

Philosophers of Science Cladogram/Monophylum Goodness-of-Fit would ask: direct “Why Popperian

direct

do indirect you

care at all?”

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Contemporary

Type of Hypothesis

Type of Test

in Theory: Philosophers ofYES Science Cladogram/Monophylum Goodness-of-Fit would ask: direct “Why

indirect do in Practice: usuallyyou NO Popperian

direct

care at all?”

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Cladogram Falsifiability: Contemporary

YESType of Hypothesis

in Theory: Philosophers ofYES Science Cladogram/Monophylum Type of Test

Goodness-of-Fit direct indirect Cladogram Rejection: would ask: “Why do in Practice: usuallyyou NO Popperian

direct

care at all?” usually NO

indirect

Hypothesis Testing in Phylogenetics using Strata Data

Theropod Origin of Birds Hypothesis Fossils from most bird-like (i.e. feathered) nonavian Theropods are younger in Age than Archaeopteryx 120 million vs 155 million

Feduccia (1994) The Great Dinosaur Debate. Living Bird 13: 29-33. Witmer (1995) The Search for the Origin of Birds. Franklin Watts, NY. Feduccia (1996) The Origin and Evolution of Birds. Yale University Press. Witmer (2002) The Debate on Avian Ancestry; Phylogeny, Function and Fossils. In: Mesozoic Birds. Pp.3-30.

Hypothesis Testing in Phylogenetics using Strata Data

Theropod Origin of Birds Hypothesis Fossils from most bird-like (i.e. feathered)

The Temporal Paradox

nonavian Theropods are younger in Age than “You can’t be Archaeopteryx

your own Grandmother”

120 million vs 155 million

Feduccia (1994) The Great Dinosaur Debate. Living Bird 13: 29-33. Witmer (1995) The Search for the Origin of Birds. Franklin Watts, NY. Feduccia (1996) The Origin and Evolution of Birds. Yale University Press. Witmer (2002) The Debate on Avian Ancestry; Phylogeny, Function and Fossils. In: Mesozoic Birds. Pp.3-30.

Hypothesis Testing in Phylogenetics using Strata Data

Theropod Origin of Birds Hypothesis Fossils from most bird-like (i.e. feathered)

The Temporal Paradox “explained” by

nonavian Theropods are younger in Age than

convergent “You can’t be Archaeopteryx Evolution & poor your own Grandmother” Fossil Record 120 million vs 155 million

Feduccia (1994) The Great Dinosaur Debate. Living Bird 13: 29-33. Witmer (1995) The Search for the Origin of Birds. Franklin Watts, NY. Feduccia (1996) The Origin and Evolution of Birds. Yale University Press. Witmer (2002) The Debate on Avian Ancestry; Phylogeny, Function and Fossils. In: Mesozoic Birds. Pp.3-30.

Hypothesis Testing in Phylogenetics using Strata Data

Theropod Origin of Birds Hypothesis DUHEM-QUINE PROBLEM Fossils from most bird-like (i.e. feathered)

The Temporal Paradox Whereas the Set “explained” by nonavian Theropods are younger in Age than {convergent HYPOTHESIS, “You can’t be Archaeopteryx BACKGROUND KNOWLEDGE, Evolution & poor your own OBSERVATIONS} Grandmother”

Fossil Record

can be falsified a whole, no 120 million vs 155as million single component of the set can be falsified in principle. Feduccia (1994) The Great Dinosaur Debate. Living Bird 13: 29-33. Witmer (1995) The Search for the Origin of Birds. Franklin Watts, NY. Feduccia (1996) The Origin and Evolution of Birds. Yale University Press. Witmer (2002) The Debate on Avian Ancestry; Phylogeny, Function and Fossils. In: Mesozoic Birds. Pp.3-30.

Hypothesis Testing in Phylogenetics using Strata Data

Theropod Origin of Birds Hypothesis DUHEM-QUINE PROBLEM Fossils from most bird-like (i.e. feathered)

The Temporal Paradox Whereas the Set “explained” by Popperian Falsificationism nonavian Theropods are younger in Age than

{convergent HYPOTHESIS,

“You can’t be Archaeopteryx BACKGROUND KNOWLEDGE, Evolution & poor your own in scientific practice usually OBSERVATIONS} Grandmother”

Fossil Record

can be falsified as a whole, no 120 million vs 155 million of NO RELEVANCE single component of the set can be falsified in principle. Feduccia (1994) The Great Dinosaur Debate. Living Bird 13: 29-33. Witmer (1995) The Search for the Origin of Birds. Franklin Watts, NY. Feduccia (1996) The Origin and Evolution of Birds. Yale University Press. Witmer (2002) The Debate on Avian Ancestry; Phylogeny, Function and Fossils. In: Mesozoic Birds. Pp.3-30.

PLAUSIBILITY TESTS for Cladograms

Plausibility Tests for Cladograms

So far it seems that so called Plausibility Tests in Phylogenetics

are indirect Tests that only function as some sort of Control:

Plausibility Tests for Cladograms

So far it seems that so called Plausibility Tests in Phylogenetics

are indirect Tests that only function as some sort of Control: congruent with Cladogram

Plausibility Tests for Cladograms

So far it seems that so called Plausibility Tests in Phylogenetics

are indirect Tests that only function as some sort of Control: congruent with Cladogram

Confirmation

Plausibility Tests for Cladograms

So far it seems that so called Plausibility Tests in Phylogenetics

are indirect Tests that only function as some sort of Control: congruent with Cladogram incongruent with Cladogram

Confirmation

Plausibility Tests for Cladograms

So far it seems that so called Plausibility Tests in Phylogenetics

are indirect Tests that only function as some sort of Control: congruent with Cladogram

Confirmation

incongruent with Cladogram

Go back …

Other Sources for Testing Cladograms: ANCESTRAL STATES

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States If the best Cladogram Hypothesis entails the Ancestral State: Wingless with blue wing Feather

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States If the best Cladogram Hypothesis entails the Ancestral State: Wingless with blue wing Feather The Hypothesis is necessarily wrong, since it is logically inconsistent.

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States If the best Cladogram Hypothesis entails the Ancestral State: Wingless with blue wing Feather The Hypothesis is necessarily wrong, since it is logically inconsistent. The Hypothesis must be rejected.

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States If the best Cladogram Hypothesis entails the Ancestral State:

This is no Wingless with blue wing Feather

The Hypothesis is necessarily wrong, Falsification! since it is logically inconsistent. The Hypothesis must be rejected.

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States Wingless with blue wing Feather

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States Wingless with blue wing Feather

Results from Violation of the Premise of Character Independence and thus incorrect Character Coding:

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States Wingless with blue wing Feather

Results from Violation of the Premise of Character Independence and thus incorrect Character Coding: Wing Feather Color [multist]

logically depends on Wing [a/p].

Hypothesis Testing in Phylogenetics using Ancestral States

Impossible Ancestral States Wingless with blue wing Feather

Check Results fromError Violation of the Premise of Character Independence and thus incorrect Coding: NoCharacter Plausibility Test Wing Feather Color [multist]

logically depends on Wing [a/p].

SUMMARY

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish : 1) direct Goodness-of-Fit Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish : 1) direct Goodness-of-Fit Tests 2) direct Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish : 1) direct Goodness-of-Fit Tests 2) direct Popperian Tests 3) internal Consistency Checks

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish : 1) direct Goodness-of-Fit Tests 2) direct Popperian Tests 3) internal Consistency Checks

4) indirect Goodness-of-Fit Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish : 1) direct Goodness-of-Fit Tests 2) direct Popperian Tests 3) internal Consistency Checks

4) indirect Goodness-of-Fit Tests 5) indirect Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2) direct Popperian Tests 3) internal Consistency Checks

4) indirect Goodness-of-Fit Tests 5) indirect Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2)Not direct Popperian applicable in Tests Cladistic Analyses 3) internal Consistency Checks

4) indirect Goodness-of-Fit Tests 5) indirect Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2)Not direct Popperian applicable in Tests Cladistic Analyses 3) internal Consistency Functions as an Checks Error Check

4) indirect Goodness-of-Fit Tests 5) indirect Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2)Not direct Popperian applicable in Tests Cladistic Analyses 3) internal Consistency Functions as an Checks Error Check

4) indirectFunctions Goodness-of-Fit Tests as a Control 5) indirect Popperian Tests

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2)Not direct Popperian applicable in Tests Cladistic Analyses 3) internal Consistency Functions as an Checks Error Check

4) indirectFunctions Goodness-of-Fit Tests as a Control 5) indirect Popperian Tests

Functions as a Control

Hypothesis Testing for Cladograms

Hypothesis Testing for Cladograms We can distinguish :

Cladistic Analyses 1) direct Goodness-of-Fit Tests 2)Not direct Popperian applicable in Tests Cladistic Analyses 3) internal Consistency Functions as an Checks Error Check

4) indirect Function Goodness-of-Fit Tests as a Control

Plausibility 5) indirect Popperian TestsTests Function as a Control

PLAUSIBILITY TESTS for Cladograms

Plausibility Tests for Cladograms

Plausibility Tests for Cladograms Plausibility Tests are independent Tests with

a new Data Source.

Plausibility Tests for Cladograms

Plausibility Tests for Cladograms Plausibility Tests are independent Tests with

a new Data Source. They function as a Control.

Plausibility Tests for Cladograms

Consequences from Plausibility Tests Two possible Results:

Plausibility Tests for Cladograms

Consequences from Plausibility Tests Two possible Results:

congruent with Cladogram

Confirmation

Plausibility Tests for Cladograms

Consequences from Plausibility Tests Two possible Results:

congruent with Cladogram

Confirmation

incongruent with Cladogram

Go back …

Plausibility Tests for Cladograms

Consequences from Plausibility Tests Two possible Results:

congruent with Cladogram

Confirmation, Confirmation BUT…

incongruent with Cladogram

Go back …

Plausibility Tests for Cladograms

Plausibility Tests for Cladograms All Plausibility Tests are indirect (extrinsic) Tests that are based on indirect Evidence.

Plausibility Tests for Cladograms

Plausibility Tests for Cladograms Problem All Plausibility Tests are indirect (extrinsic) Evaluating indirect Evidence usually Tests that are based on indirect Evidence. involves auxiliary Assumptions

Plausibility Tests for Cladograms

Plausibility Tests for Cladograms Problem All Plausibility Tests are indirect (extrinsic) Evaluating indirect Evidence usually Tests that are based on indirect Evidence. involves auxiliary Assumptions

Plausibility Tests for Cladograms

Plausibility Tests Plausibility Tests can be seen as

methodologically not integrated analytical Approaches.

Plausibility Tests for Cladograms

Plausibility Tests Plausibility Tests can be seen as

methodologically not integrated analytical Approaches. They lack a Rationale for Weighting Evidence that is

compatible with the Model used for Reconstructing Phylogenies.

Plausibility Tests for Cladograms

Plausibility Tests Plausibility Tests can be seen as

Lack of a UNIVERSAL

methodologically not integrated analytical

WEIGHTING SCHEME Approaches. covering all types for of They lack a Rationale Weighting Evidence relevant Data that is

compatible with the Model used for Reconstructing Phylogenies.

Plausibility Tests for Cladograms

Plausibility Tests Plausibility Tests can be seen as

Lack of a UNIVERSAL

methodologically not integrated analytical

We possess only WEIGHTING SCHEME Approaches. covering all types for of They lack Rationales a Rationale local Weighting Evidence relevant Data that is

compatible with the Model used for Reconstructing Phylogenies.

Plausibility Tests for Cladograms

Plausibility Tests Plausibility Tests can be seen as

Lack of a UNIVERSAL The General Problem of methodologically not integrated analytical

We possess only WEIGHTING SCHEME Approaches. all Total Evidence covering all types for of They lack a Rationale local Rationales Approaches! Weighting Evidence relevant Data that is

compatible with the Model used for Reconstructing Phylogenies.

CONCLUSION

Conclusion

Plausibility Tests… …are of limited Importance in Phylogenetics, because their Contribution to Decision Making

is very limited!

Conclusion

Plausibility Tests… In terms of Decision Making

…are of limited Importance in Phylogenetics,

regarding the Choice of the currently because their Contribution to Decision Making

Cladogram, Plausibility Tests is verybest limited! have no actual Function!

Conclusion

Plausibility Tests… …are of limited Importance in Phylogenetics, because their Contribution to Decision Making …neither in terms of

is very limited!

Falsification / Corrobration,

Conclusion

Plausibility Tests… …are of limited Importance in Phylogenetics, because their Contribution to Decision Making …nor in terms of

is very limited!

Degree of Support.

Conclusion

Plausibility Tests… …are of limited Importance in Phylogenetics, Plausibility “Tests” do NOT

because their Contribution to Decision Making rd provide a 3 , alternative

is very limited!

Approach to Hypothesis Testing

Conclusion

Indirect Evidence…

Conclusion

Indirect Evidence… …can be relevant for Cladistic Analyses, but requires the development of an appropriate

methodological framework for its Evaluation in comparison to direct Evidence!

Hypothesis Testing

Obsession with Cladograms “The Map is more interesting than the Territory”

Hypothesis Testing

Obsession with Cladograms “The Map is more interesting than the Territory” We seem to be more interested in “(…) the world as juxtaposition” than in “(…) the world as narrative” .

Hypothesis Testing

Obsession with Cladograms “The Map is more interesting than the Territory” We seem to be more interested in “(…) the world as juxtaposition” [a list] than in “(…) the world as narrative” [the history] .

Hypothesis Testing

Obsession with Cladograms Ronald Jenner’s distinction of: chronicle narrative

tree & tree construction

Hypothesis Testing

Obsession with Cladograms Ronald Jenner’s distinction of: chronicle narrative

tree & tree construction vs

historical narrative

tree interpretation & reconstruction of character evolution

Hypothesis Testing

Obsession with Cladograms Ronald Jenner’s distinction of: chronicle narrative tree & treeHypotheses construction Testing Cladogram/Monophyly vs

historical narrative

tree interpretation & reconstruction of character evolution

Hypothesis Testing

Obsession with Cladograms Ronald Jenner’s distinction of: chronicle narrative tree & treeHypotheses construction Testing Cladogram/Monophyly vs tree interpretation & historical narrative reconstruction Science after the Tree of character evolution

SCIENCE AFTER THE TREE We should use cladograms more often to test other evolutionary hypotheses

SCIENCE AFTER THE TREE We should use cladograms more often to test other evolutionary hypotheses e.g. for testing general evolutionary hypotheses as for instance “transformation rates correlate with habitat temperature”

Hypothesis-Testing in Phylogenetics: Falsification vs. Measures of Goodness-of-Fit, and the Question of the Possibility of “Plausibility-Tests“ Lars Vogt, Uni Bonn

THANK YOU FOR YOUR ATTENTION Acknowledgements Alex Gruhl Ronald Jenner Björn Quast Christoph Bleidorn