-
PHILOSOPHY OF BIOLOGICAL SYSTEMATICS
Kirk Fitzhugh, [email protected]
Table of Contents
Introduction
.........................................................................................................................
2
The Goal of Science. The goal of Biological Systematics
....................................................... 10
Causal Relationships in Systematics
....................................................................................
52
The Nature of Why-Questions
.............................................................................................
63
The Three Forms of Inference: Deduction, Induction, Abduction
......................................... 83
The Uses of Deduction, Induction, and Abduction in Science
.............................................. 110
Systematics Involves Abductive Inference
..........................................................................
155
Inferences of Systematics Hypotheses, i.e. Taxa
..................................................................
176
Some Implications for Phylogenetic Methods
.................................................................
228
The Requirement of Total Evidence
....................................................................................
336
Homology & Homogeny & Homoplasy
...............................................................................
403
Character Coding
...............................................................................................................
466
The Mechanics of Hypothesis Testing in Biological Systematics
.......................................... 500
Implications for Nomenclature
...........................................................................................
627
Defining Biodiversity and Conservation
..............................................................................
683
mailto:[email protected]
-
THE PHILOSOPHY
OF
BIOLOGICAL SYSTEMATICS
Kirk Fitzhugh
[email protected]
Natural History Museum of Los Angeles County
This course differs from most courses on biological systematics
in that the emphasiswill not be on instructing you on how to use
the variety of methods available toresearchers. Instead, the
emphasis will be on examining what is required to ensurethat
systematics, as a field of science, has an overarching framework
that isconsistent with all fields of scientific inquiry. It is from
this framework that one canreadily decide which methods are
scientifically acceptable.
-
The Philosophy of Biological Systematics
The contrast with a systematics course
A TYPICAL PHYLOGENETICS COURSE:
Phylogenetic theory
Characters and character coding
Tree building techniques
Tree statistics and tree support
Bayesian inference
Maximum Likelihood
Alignment
Molecular Dating Various tree building programs (e.g., MrBayes,
POY, and TNT)
P Systematics courses usuallyfocus on how to use methods.
P The present course will focuson what is required to
treatsystematics as a science.
P The goal is to give you the abilityto determine which methods
arescientifically acceptable.
The outline of topics shown here formed the basis for a recent
'phylogenetics'course in Denmark. The topics exemplify how the
present course differs from whatis typically covered in systematics
courses.
-
If science is not to degenerate into amedley of ad hoc
hypotheses, it mustbecome philosophical and must enterinto a
thorough criticism of its ownfoundations.
Alfred North Whitehead (1925: 25),Science and the Modern
World.
One of the interesting phenomena surrounding the practice of
systematics for thepast 40 years is that distinct schools of
thought have arisen regarding what it meansto infer systematics
hypotheses and to evaluate them. For instance, with regard
tophylogenetic [sic] inference, the two most recognized schools of
thought are whatare said to be 'parsimony' and 'maximum
likelihood.' Or, this dichotomy issometimes seen as a distinction
between hypothetico-deductive and statisticalpoints of view. One of
the hallmarks of these different opinions is that no
criticalassessment of the formal inferential structure of
systematics is ever considered,such that neither the concept of
parsimony nor likelihood are correctly justified.This lack of
critical examination then extends to the matter of how one
tests,evaluates, determines support, etc., for systematics
hypotheses.
As indicated in the quote shown here, in order to address the
matter of how we areto assess whether or not one systematics
hypothesis is better or worse than anotherrequires that we
carefully examine the philosophical foundations of
hypothesisinference and testing.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
This course is arranged in four parts. Part 1 has as its focus
identifying the goals ofscientific inquiry and biological
systematics, followed by some of the consequencesof those goals.
The three recognized forms of reasoning used throughout thesciences
are then described in detail.
-
The Philosophy of Biological Systematics
Course Outline Part 2
1. Systematics involves abductive inference.
2. Inferences of systematics hypotheses, i.e. taxa.
3. Some implications for phylogenetic methods.
In Part 2, we will identify the type of reasoning used in
biological systematics toinfer hypotheses. We will see that all
taxa have the form of explanatory hypotheses,directed at giving us
at least initial causal understanding of some of the characterswe
observe among organisms. Significant implications are then
identified for someof the methods commonly used in phylogenetic
[sic] systematics.
-
The Philosophy of Biological Systematics
Course Outline Part 3
1. The requirement of total evidence.
2. Homology & homogeny & homoplasy.
3. Character coding.
4. The mechanics of hypothesis testing in biological
systematics.
Part 3 will address four different issues, all of which have
received considerableattention in biological systmeatics, but also
have been misrepresented.
We will examine the correct interpretation of the requirement of
total evidence,which has significant implications for the common
approach of inferringsystematics hypotheses from partitioned data,
as well as attempts to comparecladograms inferred from different
data sets.
Next we will examine the definition of the term homology (sensu
Owen) in relationto E. Ray Lankester's (1870) suggested replacement
of that term with the two terms,homogeny and homoplasy.
A general overview of character coding will then be presented as
it relates to thenature of our observation statements,
why-questions, and the goal of biologicalsystematics reasoning.
Finally, the nature of hypothesis testing will be carefully
examined, showing thattraditional attempts to characterize testing
in systematics have been incorrect. Theproper approach to testing
systematics hypotheses will be examined.
-
The Philosophy of Biological Systematics
Course Outline Part 4
1. Implications for nomenclature.
2. Defining biodiversity and conservation.
In the final part of the course, we first will examine the
implications of theinferential framework for biological systematics
on our nomenclatural practices.The main focus here will be on the
'Linnean' system and the PhyloCode, to showthat neither approach
correctly takes into consideration the nature of our inferences.For
any nomenclatural system to be successful, it must be consistent
with the factthat biological systematics is about inferring
explanatory hypotheses, referred to astaxa, and formal names must
refer to those hypotheses, not just organisms.
The last talk will be an opportunity to tie our systematics
practices, as presented inthis course, to new formal definitions of
biodiversity and conservation.Interestingly, the outcome will be to
show that the term biodiversity is largelyuseless and potentially
deceptive.
-
Science depends on judgments of thebearing of evidence on
theory.... Oneof the central aims of the philosophyof science is to
give a principledaccount of those judgments andinferences
connecting evidence totheory.
Peter Lipton (2001: 184, Inference to the bestexplanation). In:
A Companion to the Philosophyof Science.
The quote shown here epitomizes what will be most fundamental
throughout thiscourse. Our emphasis will be on recognizing the
relations between evidence andbiological systematics hypotheses. As
we will see, these relations occur in differentways, depending on
what we mean by 'evidence,' as well as our objectives inmaintaining
particular relations. It is by applying the principles of
philosophy ofscience to biological systematics that we can clearly
understand why these relationsexist between evidence and
hypotheses, and recognize the forms evidence takeswith respect to
hypotheses.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
Let's start by looking at the goals of science and biological
systematics.
-
characterweighting?
measures ofsupport?
total evidence?hypothesistesting?
What is the philosophicalbasis for choosing a method?
The Confusing Variety of Systematics Methods
What are species? What are taxa?
One of the greatest difficulties in biological systematics is
that we have available avariety of methods. But, there is no clear
consensus among systematists as to whichmethods to use. Similarly,
there are fundamental questions regarding what we meanby terms like
'species' or 'taxon.'
The only real way to resolve these problems is to have a
philosophical basis forchoosing among methods. That basis can only
come from first ackowledging thegoal of doing science, and then
applying that goal to systematics.
-
Basic Criteria for JudgingMethods in Biological Systematics
Recognize the goal of Science.
The goal of biological systematics should beconsistent with this
goal.
Does a particular systematics method satisfy thegoal of
Science?
Does a particular systematics method accuratelyrepresent our
perceptions and why-questions?
To determine whether or not an approach to biological
systematics is scientificallyappropriate, we must first acknowledge
the goal of doing science, as well asunderstand that the goal of
systematics must be consistent with that more generalgoal. We can
then determine whether or not specific methods actually serve
tofulfill both the goal of science as well as systematics. In
related fashion, we have toensure that the methods we use do
accurately represent our observation statementsand why-questions,
since these are the issues to which the goal of science inquiry
isdirected.
-
Broadly speaking, the vocabulary of science has two
basicfunctions: first, to permit an adequate description of the
thingsand events that are the objects of scientific
investigation;second, to permit the establishment of general laws
or theoriesby means of which particular events may be explained
andpredicted and thus scientifically understood; for to understanda
phenomenon scientifically is to show that it occurs inaccordance
with general laws or theoretical principles.
Hempel (1965: 139, emphasis original), Aspects ofScientific
Explanation
The Goal of Science: To Causally UnderstandWhat We Observe
An answer to the question of what is the goal of science was
nicely described by thephilosopher of science, Carl G. Hempel. The
goal can be identified as having twoparts: (1) describing the
objects and events we encounter, and (2) presentingexplanations of
those objects and events, for the purpose of ever-increasing
ourunderstanding as well as having the ability to make predictions
into the future.
Overall, the goal of science is to enable us to *causally
understand* phenomena. Aswe will see throughout this course, this
goal will be the highest priority forbiological systematics.
-
The Goal of Science: To Causally UnderstandWhat We Observe
Scientific inquiry has two fundamental components:
Descriptive: Theoretical:
observations inferences of hypotheses and theories
Based on Hempel's characterization of science, we recognize
science as having twobasic parts: 'descriptive' and 'theoretical.'
The descriptive component refers to ourcommunicating observations,
as observation statements. The theoretical refers toour
applications of theories and hypotheses to those observation
statements.
-
Scientific inquiry has two fundamental components:
The Goal of Science: To Causally UnderstandWhat We Observe
The descriptive and theoretical aspects of inquiry are
interdependent objects and events cannot be described in the
absence of theory, and thebasis for theories and hypotheses are the
objects and events which are in
need of understanding.
Descriptive: Theoretical:
observations inferences of hypotheses and theories
But, it is well known that observation statements cannot be made
in the absence oftheories, and theories and hypotheses have their
origins in observations. So, thedescriptive and theoretical realms
are clearly interdependent.
-
Scientific inquiry has two fundamental components:
Understanding
The Goal of Science: To Causally UnderstandWhat We Observe
explanation / prediction
It is the interplay between the descriptive and theoretical
thatleads to scientific understanding.
Descriptive: Theoretical:
observations inferences of hypotheses and theories
As the principle goal of scientific inquiry is to acquire causal
understanding, andfrom that understanding we have the ability to
explain phenomena as well as makepredictions of future phenomena,
it is the interplay between the descriptive andtheoretical that
leads to the acquisition of understanding.
-
Scientific Understanding, Defined
A phenomenon P can be under-stood if a theory T of P exists
thatis intelligible (and meets the usuallogical, methodological and
empi-rical requirements).
de Regt & Dieks (Synthese 2005: 150)
We have been referring to 'understanding' in the previous
diagrams, so it will beuseful to have a formal definition of the
term. The definition shown here offers theview that to understand a
phenomenon is to associate that phenomenon with sometheory.
-
...the cognitive achievement realiz-able by scientists through
theirability to coordinate theoreticaland embodied knowledge that
applyto a specific phenomenon.
Leonelli (2009: 197)
Scientific Understanding, Defined
Leonelli (2009) offers a similar perspective with regard to
biological understanding.We apply not only our theories but also
our previous established knowledge to aphenomenon to provide us
understanding of the latter.
-
1904-2005
...biology can be divided into thestudy of proximate causes, the
sub-ject of the physiological sciences(broadly conceived)
Mayr (1982: 67)
, and into thestudy of ultimate (evolutionary)causes, the
subject matter ofnatural history....
Even within biology, there have been attempts to characterize
the nature of theunderstanding we seek regarding organisms. An
excellent and very usefulcharacterization of biological
understanding was developed by evolutionarybiologist, Ernst
Mayr.
Mayr suggested that biological inquiry seeks to acquire
understanding that is causal,and that such causal understanding can
be separated into 'proximate' and 'ultimate'causes. While Mayr
distinguishes proximate and ultimate causes as related
to'physiological sciences' and 'natural history,' we will need to
be more precise.
-
1904-2005
...proximate causes govern theresponses of the individual
(andhis organs) to immediate factorsof the environment while
ultimatecauses are responsible for theevolution of the particular
DNAcode of information with whichevery individual of every
speciesis endowed. Mayr (1961: 1503)
Mayr originally published his idea of proximate and ultimate
causes in biology in1962. What might be noticed is that proximate
causes refer to those causes that onlyoccur within an organism
during its lifetime. Ultimate causes, on the other hand,transcend
lifetimes.
-
Beatty (1994: 334)
The proximate causes of anorganisms traits occur within
thelifetime of the organism....
The ultimate causes occur prior to thelifetime of the organism,
within theevolutionary history of the organismsspecies.
In his analysis of Mayr's proximate/ultimate distinction, Beatty
(1994) offers a verygood characterization, shown here.
-
proximate
ontogenetic /functional
evolutionary
ultimate
Biological Understanding sensu Mayr
We can now begin to summarize Mayr's view of causal
understanding in biologywith the more general goal of science we
examined earlier. We can see thatproximate understanding refers to
ontogenetic and functional aspects during thelifetime of an
individual organism. Ultimate understanding refers to
evolutionarycauses that can apply to groups of organisms over
time.
-
descriptive biology(observation statements)
It is sometimes overlooked how essentiala component in the
methodology ofevolutionary biology the underlyingdescriptive work
is.
Mayr (1982: 70)
Goal of Science acquire ever-increasing understanding:
descriptive causal - proximate / ultimate predictive
Biological Understanding sensu Mayr
proximate
ontogenetic /functional
evolutionary
ultimate
But in addition to proximate and ultimate understanding, Mayr
was very clear in hiswritings on the subject that there is a third
dimension to understanding, what hereferred to as 'descriptive
biology.' Mayr was correct that in order to pursue eitherproximate
or ultimate understanding, one must already have observations of
effectsthat are in need of explanation. These effects are in the
form of the properties,features, characters, etc., of organisms,
that we communicate by way of ourobservation statements.
Notice that Mayr's descriptive, proximate, and ultimate
understanding areconsistent with the goal of science presented
earlier. To acquire ever-increasingunderstanding we see that it
must be descriptive as well as causal, and alsopredictive. We seek
descriptive understanding of what we perceive, as well asoffering
possible past causes that explain what we observe in the present.
And weattempt to apply our understanding into the future with
predictions of effects due tocausal conditions that exist in the
present.
-
Biological Understanding sensu Mayr
descriptive biology(observation statements)
proximate
ontogenetic /functional
evolutionary
ultimate
To what extent is biological systematicssuccessful at acquiring
ever-increasingunderstanding that is descriptive, proxi-mate, and
especially ultimate?
Mayr (1982: 70)
It is sometimes overlooked how essentiala component in the
methodology ofevolutionary biology the underlyingdescriptive work
is.
An important part of this course will be to examine the extent
to which descriptive,proximate, and ultimate understanding is
acquired in biological systematics. Thesewill be issues that need
to be addressed both in terms of knowing the nature of ourreasoning
from observations to the variety of hypotheses used in systematics,
aswell as the correct approach to testing any of those hypotheses.
It is especially theact of testing that accomplishes the task of
increasing our causal understanding,which is the most fundamental
goal of scientific inquiry.
-
Astronomy
Chemistry
Physics
Geology
Biology
Psychology
SpecializedTechniques
SpecializedTechniques
SpecializedTechniques
SpecializedTechniques
SpecializedTechniques
SpecializedTechniques
SCIENCE: General Principles and Specialized Techniques
Principles ofScientific Method
While the goal in all fields of science is the acquisition of
causal understanding, andthat must be regulated by our general
rules and methods in science, and moregenerally by philosophy of
science, each field of science must adopt its ownspecialized
techniques for the purpose of acquiring that understanding.
The problem we will identify in biological systematics, however,
is that thespecialized techniques are too often divorced from the
more general principles ofscientific inquiry and philosophy. We
will attempt in this course to correct thatproblem.
-
1. Rationality
Beliefs and actions should be rational, i.e. theyshould make
sense. A rational belief or action isone based on all evidence that
is relevant to theformation of that belief or action.
Four Fundamental Criteria Applied in Science
In order to correctly characterize the nature of biological
systematics as a fieldwithin the broader realm of science, we need
to recognize four fundamental criteriathat are applied throughout
the sciences.
The first criterion is rationality.
-
External physical world ofobjects and events
Internal mental world ofperceptions and beliefs
correspondence
Four Fundamental Criteria Applied in Science
2. Truth
Truth is a property of statements. Thecorrespondence theory of
truth is the mostcommon concept of truth applied in Science:
truestatements correspond with reality. Facts aboutthe world
determine the truth of statements.
The second criterion is truth. As noted in this slide, the
'correspondence theory' istypically used in the sciences, although
there are about six theories of truthavailable. With regard to
systematics, in which there has developed a popularculture of
thinking in terms of 'true phylogenetic trees' as a basis for
judgingmethods of cladogram inference, it should be apparent that
truth cannot be assertedseparate from some empirical basis for the
truth of statements.
-
Four Fundamental Criteria Applied in Science
3. Objectivity
The existence of objects and events apart fromhuman minds.
Objective knowlege is concernedwith physical objects and
events.
The third criterion is objectivity, which should be
apparent.
-
Four Fundamental Criteria Applied in Science
4. Realism
The correspondence of human perceptions withthe external and
independent (and possiblyunobservalbe) realities of physical
objects andevents.
And finally there is the criterion of realism.
-
Common Sense
Common Sense: The assumption that physical reality exists.
The Foundations of Science
As we have already noted, the ultimate goal of science is to
acquire ever-increasingcausal understanding of the phenomena
(objects and events) we encounter. Tosuccessfully achieve that
goal, we have to recognize the hierarchical structurewithin which
science resides as part of human reasoning.
The most general rule we have is that of common sense. In other
words, we operateunder the assumption that physical reality does
exist - that all that we perceivearound us are not just
hallucinations. Without this assumption, empirical inquiry ofany
kind would not be possible.
-
Common Sense
Philosophy
Philosophy: The study of the way humans think and
reason.Composed of four main branches:
logic, the study of reasoning
epistemology, the study of knowledge
metaphysics, the study of concepts and their relations
ethics, the study of moral evaluation
The Foundations of Science
Within the realm of common sense, we have the field known as
philosophy - thestudy of the way humans think and reason. And
within philosophy there are fourbranches.
-
Common Sense
Philosophy
Philosophy of Science
Philosophy of Science: The study of the principles and
methodsapplied in all fields of science.
The Foundations of Science
The four branches of philosophy presented in the previous slide
are often applied tothe subfield of philosophy, known as philosophy
of science, which studies theprinciples and methods used throughout
the sciences.
-
Common Sense
Philosophy
Philosophy of Science
Scientific Methods
Scientific Methods: The processes of hypothesis and
theoryformation, testing, and revision, for thepurpose of acquiring
understanding ofphysical reality.
The Foundations of Science
It is by way of philosophy of science that scientific methods
are developed. It isthose methods that are intended to enable us to
achieve the goal of scientificinquiry, i.e. causal
understanding.
-
Common Sense
Philosophy
Philosophy of Science
Scientific Methods
Scientific Specialties
Scientific Specialties: The fields of study that address
specificaspects of physical reality, e.g., physics,chemistry,
paleontology, systematics.
The Foundations of Science
By way of particular scientific methods there are the
applications of scientificspecialities.
-
Common Sense
Philosophy
Philosophy of Science
Scientific Methods
Scientific Specialties
Technology
Technology: The specialized techniques appliedin a specific
field of study.
The Foundations of Science
The applications of scientific methods within scientific
specialities are often onlypossible because of technology, e.g.
computers, microscopes, etc.
-
Common Sense
Philosophy
Scientific Specialties
Technology
Scientific Methods
Philosophy of Science
The Foundations of Science
Scientific methods are constrained by the principles of
philosophy, as wellas the philosophy of science. The problem in
systematics is that methodsare too often developed and considered
in isolation of philosophy.
Finally, it is important to notice that if we are going to
critically evaluate ourscientific methods, then this must be done
in the context of philosophy of science aswell as philosophy in
general. Scientific methods cannot operate independent
ofphilosophical principles. Unfortunately, this is exactly what has
too often occurredin biological systematics. This course is
intended to help correct that error.
-
What is the Goal of Biological Systematics?
C To explain shared similarities among a group of organisms.
Some common answers
We have seen that the goal of scientific inquiry is to not only
describe the objectsand events we encounter (observation
statements), but more importantly to causallyunderstand those
phenomena. We now need to determine if the goal of
biologicalsystematics is consistent with the goal of science.
When we ask the question, 'What is the goal of systematics?',
there are at least threegeneral answers given. What you will notice
is that most of these answers are notconsistent with the goal of
science. And this is a serious problem.
One answer to the question we sometimes encounter is that
systematics is intendedto explain shared similarities.
-
Parsimony [sic]
A genealogy is able to explainobserved points of similarity
amongorganisms just when it can accountfor them as identical by
virtue ofinheritance from a commonancestor.
Farris (1983: 18), The logical basis ofphylogenetic analysis
The idea of explaining shared similarities has been especially
common in thecontext of cladograms. Unfortunately, this notion is
not usually extended to otheraspects of systematics, as we will see
later in this course.
The idea of explanation in systematics has been common in the
cladistics literature,especially in connection with the principle
of parsimony.
-
Likelihood [sic]
The concept of likelihood refers tosituations that typically
arise innatural sciences in which givensome data D, a decision must
bemade about an adequateexplanation of the data.
Schmidt & von Haeseler (2010: 181),Phylogenetic inference
using maximumlikelihood methods.
But we also find claims that explanation is important when
'likelihood' methods areused. But as we will see later in this
course, these claims of importance ofexplanation are too often
poorly formulated and usually insufficient.
-
What is the Goal of Biological Systematics?
C To explain shared similarities among a group of organisms.
Some common answers
C To show the phylogeny / evolutionary history of a group
oforganisms.
A much more vague reference to explanation being the goal of
systematics comesfrom the popular view that we want to present
'phylogeny' or 'evolutionary history.'
-
Systematics is the study of organicdiversity as that diversity
is relevantto some specified pattern ofevolutionary relationship
thought toexist among the entities [sic]studied.
Wiley & Lieberman (2011: 8),Phylogenetics: Theory and
Practice ofPhylogenetic Systematics
And as we see in this quote, even the explain-as-phylogeny point
of view can betaken to a point of being uninformative.
-
A phylogenetic tree [cladogram]...is a graphic representation of
thehistorical course of speciation.
Wiley & Lieberman (2011: 4),Phylogenetics: Theory and
Practice ofPhylogenetic Systematics
And the explanatory nature of cladograms is often
inconsistent.
-
What is the Goal of Biological Systematics?
C To explain shared similarities among a group of organisms.
C To discover natural, hierarchical order, then reflect that
orderin classifications.
Some common answers
C To show the phylogeny / evolutionary history of a group
oforganisms.
Rather than having a direct or indirect goal of explanation of
systematics, there isthe still-popular school of thought that
causality should be removed fromsystematics. In this instance,
diagrams such as cladograms have no explanatoryinterpretation, but
instead either summarize character distributions, or conveynebulous
ideas such as 'natural order' or 'natural hierarchies.' The general
phrasecommonly used to identify this less-than-scientific
perspective is 'pattern cladistics.'
-
Systematics is primarily concernedwith problem solving. This
mightseem an obvious statement, yet themajority of those interested
insystematics and phylogenyapproach the subject as beingconcerned
with inferences,reconstructions, or estimations....
Williams & Ebach (2008: 21)Williams & Ebach (2008:
21)
The general problem may bephrased as follows: What are
theinterrelationships amongorganisms?
The pattern cladistic approach has serious problems in that it
is inconsistent withthe goal of scientific inquiry.
-
What is the Goal of Biological Systematics?
C To explain shared similarities among a group of organisms.
C To discover natural, hierarchical order, then reflect that
orderin classifications.
Some common answers
C To show the phylogeny / evolutionary history of a group
oforganisms.
ARE ANY OF THESE GOALS CONSISTENT WITH THEOVERALL GOAL OF
SCIENCE?
Based on what we have already seen regarding the goal of
scientific inquiry, thecommonly identified goals of biological
systematics are not sufficiently consistentwith the goal required
of all sciences.
-
What is the Goal of Biological Systematics?
A Formal Definition of Biological Systematics
The actions of biological systematization. The goal of which
isto obtain causal understanding of the properties or charactersof
organisms exhibited at different stages of their life history
orshared among some set of individuals.
The term taxonomy is unnecessary because it is a synonym
ofsystematics.
To correctly and effectively identify the goal of biological
systematics requires thatthis goal be fully consistent with the
more general goal of scientific inquiry. Shownhere is a formal
definition of biological systematics that not only places it
squarelyin the realm of science, but also establishes the field as
having the same goal as allfields of science: to acquire causal
understanding of the features we observe oforganisms.
Notice that with this formal definition, we no longer need to
make a distinctionbetween the terms 'systematics' and 'taxonomy.'
While some might think thattaxonomy refers only to 'species
descriptions,' as we will see during this course, allfacets of
systematics have the same inferential framework, wherein all
actions insystematics are directed at achieving the goal of causal
understanding. Taxonomy isa term that should be regarded as a
synonym of systematics. Systematics is the moreaccurate term to
use.
-
What is the Goal of Biological Systematics?
Any of a set of classes of hypotheses used in biological
syste-matics for the purpose of explaining particular characters
ofobserved organisms.
A Formal Definition of Taxon
With the formal definition of biological systematics accurately
manifesting the goalof scientific inquiry, it is crucial that our
reference to a taxon also be consistent withthat goal. Clearly, as
the goal of systematics is to present explanatory hypothesesthat
give us an opportunity to understand the occurrences of features
amongorganisms, then taxa can only be regarded as synonymous with
those hypotheses.
Of course, this will have profound consequences, because too
often taxa are thoughtof as being either individuals or things that
exist in time and space, much likeorganisms. As we will see
throughout this course, taxa can only be regarded asexplanatory
hypotheses, not as things or individuals. Indeed, our use of the
termtaxon or taxa is entirely unnecessary. It would be more
appropriate to simply referto hypotheses.
-
...the semaphoront [character bearer]corresponds to the
individual in acertain, theoretically infinitely small,time span of
its life, during which it canbe considered unchangeable.
W. Hennig (1966: 65)
The definition of taxon presented in the previous slide refers
to individualorganisms and the characters we observe. In his book,
"Phylogenetic Systematics"(1966), Willi Hennig correctly stressed
that we make observations of individuals atparticular moments in
time during their entire ontogeny or life history. Hennigsuggested
that the appropriate term for the individuals we observe should
be'semaphoront.'
-
...it follows that we should not regard theorganism or the
individual (not to speakof the species) as the ultimate element
ofthe biological system. Rather it should bethe organism or the
individual at a parti-cular point of time, or even better, duringa
certain, theoretically infinitely small,period of its life. We will
call this elementof all biological systematics...
thecharacter-bearing semaphoront.
W. Hennig (1966: 6, emphasis original)
Hennig's use of the term semaphoront to indicate our
observations of organisms atspecific times during their life
history is especially significant because it betteremphasizes that
the fundamental units in biological systematics are
individualorganisms. Indeed, notice that Hennig understands that
species are not thefundamental units in systematics.
-
Obtain causal understanding of the properties or charactersof
organisms exhibited at different stages of their life historyor
shared among some set of individuals.
What is the Goal of Biological Systematics?
Some Consequences:
Biological systematics involves the non-deductive inference
ofexplanatory hypotheses and, where possible, their
subsequenttesting.
The goal of biological systematics is to move toward
causalunderstanding of what we observe, not merely to
obtaincladograms, trees, or to reconstruct phylogeny.
Cladograms are not things in themselves, but are very
limitedexplanatory hypotheses of observed properties of
individualsamong different taxa.
With a formal definition of biological systematics that is
consistent with the goal ofscientific inquiry, there are several
significant implications.
The first is that as systematics is about the inferences of
explanatory hypotheses, wewill be clearly identifying the type of
inference involved, as well as acknowledgingthat the testing of
those hypotheses is very different from what has traditionallybeen
presented by systematists.
Second, since the goal of systematics is consistent with the
goal of science, i.e. toacquire causal understanding, our goal is
*never* to just get trees, cladograms, orreconstruct phylogeny
[sic].
And finally, we will see in this course that cladograms are
*very vague*explanatory accounts. Indeed, they are so poor as
explanations that they offer usvery little to serve as vehicles for
the goal of doing systematics, much less science.
-
Present(the realm of Observation)
Past Future
Cause
Effect
predictionEffect
ExperimentalSciences
abduction
CausalHypothesis
HistoricalSciences
The Two Realms of Science
Biological systematics is part of the historicalsciences, where
observations in the present areused to infer explanatory hypotheses
about pastevents to account for those observations.
For our purposes in biological systematics, we can think of
science as having twobroad, operational realms: historical and
experimental. The historical sciencesinclude such fields as
systematics, evolutionary biology (in part),
paleontology,archaeology. The experimental sciences include
physics, chemistry, geology (inpart). There is, of course, a lot of
overlap between these.
The main distinction between the historical and experimental
sciences is that thehistorical sciences focus on effects that exist
in the present, and our goal is todevelop explanatory hypotheses of
possible past causal events that can account forthose oberved
effects. The experimental sciences, on the other hand, begin
withknown causal, or experimental, conditions in the present, to
see if predicted effectsoccur in the future.
Another way to think about this distinction is that the
historical sciences are mainlyconcerned with the inferences and
testing of explanatory hypotheses, whereas theexperimental sciences
are mainly concerned with the testing of theories. But, becautious
about this distinction, since there always are exceptions.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
We can now take an initial look at the nature of the
relationships that are referred toin biological systematics. Since
the goal of systematics is to present us with causalunderstanding
of the features of organisms, then the nature of the
relationshipsthroughout systematics must be causal in form.
-
RELATIONSHIPS &BIOLOGICAL SYSTEMATICS
When we speak of relationships in systematics,we mean causal
relationships. The basic unitto which these causal relationships
refer is indivi-dual organisms. Taxa as explanatory hypothe-ses
indicate particular causal relationshipsamong groups of
organisms.
To start with our examination of these issues, we need to
understand what we meanwhen we speak of 'relationships' in
biological systematics. We use the termrelationship on a regular
basis, but, the word is often not clearly understood when itis used
in systematics.
We need to first recognize that when we speak of relationships,
we are speaking ofcausal relations. For example, we say we are
related to our parents, we are relatedto our sisters or brothers,
we are related to our grand parents. In every instance,
therelations we are talking about are causal relations, because it
is that type ofrelationship that gives one understanding. And, as
we will see in the remainder ofthis course, the units to which
those causal relationships refer are individualorganisms.
Then, we can specifically look at the way in which we infer each
of the types ofcausal relationships, as explanatory hypotheses,
that are used in biologicalsystematics. And again, it is causal
relationships that we are interested in, because itis those types
of relations that best serve the overall goal of scientific
inquiry.
-
Hennig, W. 1966.Phylogenetic Systematics
(1913-1976)
One of the best examinations of the nature of causal
relationships in biologicalsystematics can be found in Willi
Hennig's (1966) book, "PhylogeneticSystematics."
-
Hennig, W. 1966. Phylogenetic Systematics
Classes of Relationships
1. ontogenetic
1
2. cyclomorphic
2
3. sexual dimorphic
3
4. tokogenetic
45. polymorphic
5
6. specific
6
7. phylogenetic
7
Each of these classesof relationships refer tothe different
classes ofexplanatory hypotheseswe call taxa.
Shown here is Hennig's (1966) well known figure 6, which we
often see reproduced in other works on the principlesof biological
systematics. It is in this figure that Hennig identifies the
fundamental classes of relationships used insystematics.
But too often, what is not recognized is that Hennig pointed out
that all of these relationships deal with individualorganisms. He
discussed in great detail seven classes of relationships involving
organisms, all of which are shown inhis diagram.
Ontogenetic relationships. Where we speak of an individual at a
particular point in it's life history.
Cyclomorphic relationships. Where there are seasonal phenotypic
differences among individuals of differentgenerations.
Sexual dimorphic relationships. The phenotypic differences
between males and females.
Tokogenetic relationships. Parents producing offsrping as a
result of reproductive events (tokogeny).
Polymorphic relationships. Different phenotypes expressed among
individuals in a population.
Specific relationships. Refers to species hypotheses, accounting
for features among a group of organisms that arereproductively
isolated from other groups.
Phylogenetic relationships. The most general type of
relationship in systematics, accounting for shared featuresamong
organisms to which different species hypotheses refer, as well as
strictly asexual or strictly self-fertilizinghermphroditic
organisms. But as will be noted later in the course, because of
what classes of causal events areentailed by phylogenetic
hypotheses, such hypotheses are actually not applicable to obligate
asexual or self-fertilizinghermaphroditic organisms.
-
7 Classes of Causal Relationships
1
2
3
4
5
6
7
Descriptive Biology(observation statements)
1. ontogenetic Proximate
1
2. cyclomorphic
3. sexual dimorphic
4. tokogenetic
5. polymorphic
6. specific (species)
7. phylogenetic
Ultimate
2
3
4
5
6
7
Using Hennig's (1966) figure 6, we can clearly identify the
three broad classes ofcausal understanding recognized by Ersnt
Mayr, that were referred to earlier.
-
Semaphoronts ontogenetic hypotheses(e.g., larva, juvenile,
adult)
Individuals the objects we perceive
Kingdom
Phylum
Class phylogenetic hypotheses
Order
Family
Genus
Species specific hypotheses
Subspecies intraspecific hypotheses
Families, demes, populations tokogenetic hypotheses
Individuals the objects we perceiveIndividuals the objects we
perceiveDescriptive explanations
(observation statements)
Proximate explanations
Ultimate explanations
And here are the distributions of classes of hypotheses shown in
the previous slide,in a different arrangement.
-
Semaphoronts ontogenetic hypotheses(e.g., larva, juvenile,
adult)
Individuals the objects we perceive
Kingdom
Phylum
Class phylogenetic hypotheses
Order
Family
Genus
Species specific hypotheses
Subspecies intraspecific hypotheses
Families, demes, populations tokogenetic hypotheses
Individuals the objects we perceiveIndividuals the objects we
perceive (observation statements)
All taxa/hypotheses in biological systematicsare inferred by way
of abduction
As we saw earlier with the definition of the term 'taxon,' all
taxa are explanatoryhypotheses. All of the different classes of
hypotheses-as-taxa shown here, indicatedby the red arrows, are the
products of a type of reasoning known as 'abduction,'which we will
examine in depth later in the course. And abduction, or
abductiveinference will form the foundation for the remainder of
our examination ofsystematics in this course.
-
individuallarva, juvenile, adult
Ontogenetic, Specific, Phylogenetic
Semaphoront:an explanatory hypothesis of ontoge-netic
relationships, derived from onto-genetic theories applied to a
particularorganism. The hypothesis accountsfor features of an
organism at aparticular age relative to features atanother age, by
way of ontogeny.
Examples of Causal Relationships in Systematics
We can briefly look at three of the most common classes of
relationships referred toin biological systematics, and discussed
by Hennig (1966): semaphoront, specific(species) relationships, and
phylogenetic relationships.
A semaphoront is an individual at a specific point in time
during its life history. Inother words, it is a hypothesis that
gives us an explanatory account relative to theontogenetic history
of the individual.
-
individual
speciesa-us
Species:an explanatory hypothesis ofspecific relationships
derived fromtheories of character origin/fixationduring tokogeny,
applied to a setof semaphorants. A lineage,accounting for features
of a groupof semaphoronts relative to differ-ent features in other
semapho-ronts (in other species).
Ontogenetic, Specific, Phylogenetic
Examples of Causal Relationships in Systematics
A species is an explanatory hypothesis that refers to specific
relationships.
-
individual
speciesa-us
species b-us species c-us
b-us c-us
a-us
phylogeneticrelationships
Supraspecific Taxon:an explanatory hypothesis ofphylogentic
relationships, deriv-ed from tokogenetic, evolution-ary, and
population splittingtheories, applied to particularsemaphoronts.
Accounting, byway of phylogeny, for the samefeatures shared by
semapho-ronts among two or morespecies relative to
differentfeatures in semaphoronts ofother species.
Ontogenetic, Specific, Phylogenetic
Examples of Causal Relationships in Systematics
And a phylogenetic hypothesis refers to phylogenetic
relationships. Notice that it ismore accurate to refer to such
relationships as hypotheses as opposed to 'taxa.'
-
Phylogenetic systematics sensu Hennig (1966) only provides
causalunderstanding of the properties of groups of organisms to
which two ormore species hypotheses also refer. Explanatory
hypotheses of ontogeny,tokogeny, species, etc., represent other
levels at which causal under-standing can also be achieved, but by
using theories different from thoseapplied in phylogeny.
Not All of Systematics is Phylogenetic
As we will see, distinguishing the different classes of
explanatoryhypotheses used in systematics is fundamental to
identifying theappropriate levels at which our why-questions should
be asked andanswered.
Historically, there has been confusion regarding what is meant
by the phrase'phylogenetic systematics.' Yet, when one carefully
reads Hennig's (1966) book, it isclear that he understood
biological ('hologenetic') systematics to refer to the varietyof
explanatory hypotheses, with phylogenetic systematics only
referring to one ofthose classes of relationships.
As we will see in this course, as the goal of systematics is the
same as the goal in allfields of science, to acquire causal
understanding, to achieve such understandingcomes from different
classes of hypotheses used to answer our different
why-questions.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
All of understanding in science begins with observations and our
questionsassociated with those observations in need of being
explained. The type ofquestions most commonly asked in systematics
are known as why-questions. It isour why-questions that form the
basis for all aspects of biological systematics.
-
The scientist is not a personwho gives the right answers,he's
the one who asks theright questions.
Claude Levi-Strauss (1964)Le Cru et le Cuit
Unfortunately, when we speak of science, we almost always
neglect to consider thequestions we are actually asking, for which
we seek hypotheses and theories to giveus answers.
-
...a logic in which the answersare attended to and the
questionsneglected is a false logic.
R.G. Collingwood (1938: 31),An Autobiography
Like any endeavor, science is one we perform to achieve
particular goals. And aswith any action carried out among a group
of people, science has its socialcomponent, such that scientific
procedures tend to become standardized to the pointwhere we stop
examining the bases for what we do, and we just go through
themotions.
Biological systematics suffers from a perspective where
practitioners are seekinganswers, yet they either don't know the
questions they are asking, or they are askinginappropriate
questions. This neglect is what has allowed for the rapid
developmentof systematics methods and computer algorithms that
offer contradictoryapproaches, and with no jusification based on
the goal of using those methodsaccording to the why-questions we
should be asking.
-
Why Ask Why!!!!Questions?
To explain the phenomena in theworld of our experience, to
answerthe question why? rather than onlythe question what?, is one
of theforemost objectives of all rationalinquiry;
From: Hempel & Oppenheim (1948: 135), The logic of
explanation.Philosophy of Science 15: 135-175.
Look to the goal of scientific inquiry
and especially [for science]...to go beyond a mere description
ofits subject matter by providing anexplanation of the phenomena
itinvestigates.
By this time it is probably obvious why we ask why-questions --
because we seekcausal understanding of the phenomena we encounter.
The quote shown here, byCarl Hempel, exemplifies the reason we ask
why-questions, and the fact that suchquestions are a fundamental
part of the goal of scientific inquiry.
-
If the goal of biological systematics is to providecausal
understanding of the properties of organisms,then we must first
recognize the nature of our why-questions, to which evolutionary
theories andsystematics hypotheses provide answers.
The Foundation for All of Systematics
The Nature of Our Why-Questions
We now need to examine the specific properties of why-questions,
without whichany treatment of biological systematics would be
incomplete. As we will seethroughout much of this course, our
why-questions are fundamental components.
-
Why-Questions
Why P?
Example: Why do these specimens havelateral body wall
extensionscalled appendages?
How we usually ask them
It is essential to know the formal structure of the
why-questions we ask. We usuallythink of why-questions as simply
having the form, "Why P?", or "Why is it the casethat x is P?" This
form is, however, incomplete and thus does not fully represent
thebasis for such questions.
-
Why P in contrast to X?
PX
Example: Why do these specimens have lateral body wallextensions
(= appendages) in contrast to otherspecimens with convex body
walls?
Why-Questions
The proper form: Contrastive questions
The correct form of why-questions is that they are
'contrastive.' In other words, weask questions that contrast the
surprising or unexpected condition in need of beingexplained with
the expected condition(s) that has already been explained.
In the case of systematics-based observations, our contrastive
why-questions are ofthe form shown here.
-
Three parts: why
Why P in contrast to X?
PX
Example: Why do these specimens have lateral body wallextensions
(= appendages) in contrast to otherspecimens with convex body
walls?
Why-Questions
There are three components to why-questions. First is that such
questions areprefaced with 'why.'
-
fact
+ fact(s) + foilThree parts: why
foilWhy P in contrast to X?
PX
Example: Why do these specimens have lateral body wallextensions
(= appendages) in contrast to otherspecimens with convex body
walls?
Why-Questions
The other two components of why-questions are known as 'fact'
and 'foil.' The 'fact'is what is in need of being explained, in
contrast to the 'foil.'
-
contrast class
fact foilWhy P in contrast to X?
PX
Example: Why do these specimens have lateral body wallextensions
(= appendages) in contrast to otherspecimens with convex body
walls?
Why-Questions
Three parts: why + fact(s) + foil
+ fact(s) + foilThree parts: why
The 'fact' and 'foil' together comprise the 'contrast class' of
a contrastive why-question.
-
Example: Why do these specimens have lateral body wallextensions
(= appendages) in contrast to otherspecimens with convex body
walls?
Question: Why P in contrast to X?
Presupposition: it is true that P is the case.
Three parts: why + facts-as-presuppositions + foil
Why-Questions
Another important condition is that we assume the truth of the
observationstatement(s) that comprise the 'fact.' These facts are
then said to be presuppositions.
-
Question: Why P in contrast to X?
fact foil
Criterion for sensibility
...we evaluate the sensibility of a why questionby considering
whether the fact and foil can beviewed as [alternative] culminating
outcomes ofsome single type of natural causal process.
Barnes, E. 1994. Why P rather than Q? The curiosities of fact
and foil.Philosophical Studies 73: 3553.
Why-Questions
The choice of foil for why-questions is not arbitrary. Instead,
correctly choosing afoil requires that fact and foil are
alternative effects from a single type of causalprocess. The
following examples exemplify this requirement.
-
Question: Why did the match not ignitein contrast to
igniting?
fact foil
Common causal process: frictional surface
Criterion for sensibility
Why-Questions
In this example we have the why-question, "Why did the match not
ignite incontrast to igniting?" Notice that fact and foil trace
back to the common causalprocess of rubbing a match along a
frictional or rough surface. The why-questionseeks an explanation
for why the match did not ignite given that under theconditions we
would have expected it to ignite. The question has proper
formregarding an appropriate foil for the fact.
-
Incorrect Question: Why did the match not ignitein contrast to
breaking?
fact foil
frictional surface thumb pressure
Separate causal processes
Criterion for sensibility
Why-Questions
Here is a why-question of incorrect form. Notice that the fact
and foil would traceback to separate and different causal
processes. Explaining why the match did notignite cannot be
contrasted with why the match broke. The two conditions refer
toentirely different causal processes.
-
Complete Why-Questions
Question: Why are these matches burned, in contrast to
unburned?
fact foil
Common cause versus separate causes
There is an additional issue that we need to consider with
regard to why-questions.This is an issue that is of importance in
systematics because we observe sharedfeatures or characters among
groups of organisms. When we observe multipleeffects that have the
appearance of being correlated, we have to decide how toexplain
such correlations.
-
Complete Why-Questions
Question: Why are these matches burned, in contrast to
unburned?
Common cause versus separate causes
Common cause explanation Separate cause explanation
In the example shown here, the correlation of finding a group of
burned matchesrequires that we decide whether to answer the
why-question, "Why are thesematches burned, in contrast to
unburned?", by either a common cause explanationor by way of
separate cause explanations.
-
Complete Why-Questions
Question: Why are these matches burned, in contrast to
unburned?
Common cause versus separate causes
How to decide?
background knowledge
Making a decision to provide a common cause explanation or
separate causeexplanations requires that one take into
consideration their background knowledgeregarding such effects.
What is important to recognize is that offereng separatecause
answers will be based on a set of questions that will be different
from whatwill be required for a common cause answer.
-
Complete Why-Questions
Q1 Q2 Q3
Separate causes
A1 A2 A3
In the case of treating the observation of the burned matches as
explainable by wayof separate causes, we would treat each effect
(i.e. burned match) as leading toseparate why-questions and
separate respective answers.
-
Complete Why-Questions
Q
Common cause
A
For a common cause explanation, we regard the correlation would
be far lesssurprising if explained by a single, commmon cause.
Hence the single questionshown earlier, "Why are these matches
burned, in contrast to unburned?"
-
Complete Why-Questions
All Questions Have a Contrastive Form
The contrastive nature of why-questions, plusthe reasoning used
to answer to thosequestions, provide the strongest criteria
forcritically evaluating the methods and proceduresused in
systematics.
Any critical appraisal of biological systematics must stand on
two issues. The firstbeing the form of contrastive why-questions,
as we have just seen. The second isthat the proper form of our
why-questions then lead to inferences of answers tothose
questions.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
Now that we have identified that the goals of science and
biological systematics areboth to acquire causal understanding of
the phenomena we encounter, we next needto carefully examine the
types of reasoning used in the sciences to achieve our goal.
As we will see later in the course, these types of reasoning
will play critical roles inattempting to correctly characterize the
tasks of systematics.
-
The Fundamentals of Inference
Inference:
The act of reasoning from a statement(premise) or statements
(premises), to aconclusion or set of conclusions.
This section of the course will focus on identifying the types
of reasoning, known asinference, we use every day as well as in the
sciences.
-
Two Types of Inference HaveTraditionally Been Recognized
Deduction:
Inferences in which a conclusion drawn from a set of(true)
premises cannot contradict those premises, andtherefore must also
be true.
All humans are mortal
Kirk is human
Kirk is mortal
Traditionally, when people speak of logic as the study of
reasoning, they only makea distinction between two types of
reasoning: deductive and inductive. Let's firstlook at this
distinction, before more accurately segregating reasoning.
In this example of deduction, notice that the premises, 'All
humans are mortal' and'Kirk is human,' is separated from the
conclusion, 'Kirk is mortal,' by a single line.
-
Two Types of Inference HaveTraditionally Been Recognized
Induction:
Inferences in which similarities are identified betweenobserved
objects or events of a given class, andhypothetically extended to
unobserved objects orfuture events of that class.
Kirk is human
Kirk is mortal
All humans are mortal
In the case of an induction (or any non-deductive inference),
the premises areseparated from the conclusion, or conclusions, by a
double line.
-
Two Types of Inference HaveTraditionally Been Recognized
Deduction:
Inferences in which a conclusion drawn from a set of(true)
premises cannot contradict those premises, andtherefore must also
be true.
Induction:
Inferences in which similarities are identified betweenobserved
objects or events of a given class, andhypothetically extended to
unobserved objects orfuture events of that class.
-
hypothesish
datad
deduction
(1) Deduction: predictions of potential test consequencesderived
from the hypothesis to be tested.
Deduction & Induction
The Popular View of Their Relations
induction
h
(2) Induction: performing the test; observations of
testconsequences, providing either confirming/corroborating or
disconfirming/falsifyingevidence.
deduction induction
h
d
This diagram illustrates how people often speak of the relations
between deductionand induction in science. Starting with a
hypothesis or theory, inferred by way ofinduction, one uses
deduction to predict potential test evidence, then induction isused
in the process of testing. The view is that there are cycles of
deduction andinduction in a continual process of evaluating
theories and hypotheses.
-
Given Hypothesis Expected Data
Inferred Hypothesis Actual Data
deduction
induction
H.G. Gauch, Jr. (2003: 160), Scientific Method in Practice
Deduction & Induction
Deduction is reasoning from what is in the mind to whatis in the
world.
Induction is reasoning from what is in the world to what isin
the mind.
The Popular View of Their Relations
This is another, common view of the relation between deduction
and induction inscience.
-
The premises and conclusion(s) of an inference containstatements
that can be categorized as three possible forms:
The Structure of Inferences
Rule: a law, empirical generalization, or theory, often statinga
relation between cause and effect;
Case: a statement about a thing(s), or event(s), in the form
ofcausal or initial conditions;
Result: a statement of a consequence or effect that is relatedto
the Case.
The Basic Components
For our purposes of examining the nature of reasoning that
exists throughoutbiological systematics, we need to make more
precise distinctions between thetypes of reasoning used in science.
To compare and contrast the different types ofreasoning, we will
use a set of statements that can be used as either premises
orconclusions. These statements are referred to as Rule, Case, and
Result.
By identifying premises or conclusions as Rule, Case, and Reult,
we will find thatin addition to deduction and induction (sensu
stricto), we will also have torecognize a third type of
non-deductive reasoning, called abduction.
-
Rule: All marbles in this bag [M] are red [P].
S = subjectP = predicateM = middle term
end terms
Deduction
A Simple Example
In this example of deduction, as well as in following examples,
the components ineach of the statements comprising the premises and
conclusions are identified assubject, predicate, or 'middle term.'
The subject and predicate are sometimesreferred to as 'end terms'
since in a deductive arrangement they are present in thepremises
and conclusion. The 'middle term,' which functions as a predicate,
thenjoins together the end terms in the conclusion.
-
Rule: All marbles in this bag [M] are red [P].
S = subjectP = predicateM = middle term
end terms
Case: This marble [S] is from this bag [M & P].
Deduction
A Simple Example
Notice that 'this bag' functions as both the middle term and
predicate for the Case.
-
Rule: All marbles in this bag [M] are red [P].
S = subjectP = predicateM = middle term
end terms
Case: This marble [S] is from this bag [M & P].
Result: This marble [S] is red [P].
Deduction
A Simple Example
The predicate 'red' in the Rule, and the subject 'marble' in th
Case are broughttogether in the Result. The middle term, 'this
bag,' is only referred to in thepremises. In deduction, the middle
term serves to bring together the end terms inthe conclusion.
-
Rule: All marbles in this bag [M] are red [P].
Case: This marble [S] is from this bag [M & P].
Result: This marble [S] is red [P].
S = subjectP = predicateM = middle term
end terms
Deduction
A Simple Example
TRUE
TRUE
TRUE
Because of the form required of the premises in deduction, if
the premises are true,then the conclusion must also be true. In
other words, the conclusion is certain.
-
P
M S
(a)
PMS
completeinclusion
(b)
Rule: The marbles in this bag [M] are red [P].
Case: This marble [S] is from this bag [M & P].
Result: This marble [S] is red [P].
Deduction
Deduction has a structure wherein the 'middle term' [M] serves
to bring together thesubject [S] and predicate [P] in the
conclusion. This relationship is illustrated herein (a), where the
solid lines indicate relations stated in the premises, and the
dashedline denotes the relation provided by the conclusion. The
Euler diagram in (b)provides another representation of these
relations, where deduction is characterizedby 'complete inclusion:'
the subject [S] is a subset of the middle term [M], and thelatter
is a subset of the predicate [P].
-
Induction
A Simple Example
Case: These marbles [S] are from this bag [M & P].
Result: These marbles [S] are red [P].
With induction, the premises are comprised of the Case and
Result. Notice that thesubject [S] is present in both premises.
-
Rule: All marbles in this bag [M] are red [P].
Induction
A Simple Example
Case: These marbles [S] are from this bag [M & P].
Result: These marbles [S] are red [P].
From the premises is concluded the Rule. You might notice that
the premises state alimted set of observations, from which a
general statement is inferred. In fact, theexample looks very
similar to a statistical inference, proceeding from observationsof
a sample to a conclusion about the population from which the sample
was taken.As we will see later in the course, induction is the
principle mode of reasoning usedin statistics. And, since
statistics is about testing statistical hypotheses, we will
findthat induction is the approach taken for testing in
general.
-
Case: These marbles [S] are from this bag [M & P].
Result: These marbles [S] are red [P].
Rule: All marbles in this bag [M] are red [P].
Induction
A Simple Example
TRUE
TRUE
TRUE / FALSE
In contrast to deduction, where true premises always guarantee a
true conclusion,an inductive conclusion from true premises cannot
guarantee a true conclusion. Theconclusion is not certain; it is
only probable, as determined by the premises. Noticethat the
conclusion thus makes a claim that goes beyond what is offered by
thepremises.
-
P
M S
(a)
Case: This marble [S] is from thisbag [M & P].
Result: This marble [S] is red [P].
Rule: The marbles in this bag [M] arered [P].
partialinclusion
PSM
(b)
Induction
As shown in (a), induction differs from deduction in bringing
together the predicate[P] and middle term [M] in the conclusion by
the presence of the subject [S] in bothpremises. The Euler diagram
(b) shows induction to be a matter of 'partialinclusion.'
-
A Third Type of Inference is Often Recognized
Abduction:
Reasoning from observed effects in the present(consequents) to a
conclusion(s) of possible cause(or causes) in the past
(antecedent).
Abduction is also the form of inference used todevelop our
observation statements. As a result,abductive inference is the most
common typeof reasoning we use on a daily basis.
In addition to deduction and induction, there is a third type of
non-deductiveinference that is often recognized, called abduction.
Abduction is a form ofreasoning we use on a daily basis to infer
from observed effects to a possible causeor causes.
-
Charles Sanders Peirce(1839-1914)
Abduction
[A] hypothesis cannot be admitted,even as a hypothesis, unless
it besupposed that it would account for thefacts or some of them.
The form ofinference, therefore, is this:
The surprising fact, C, is observed;
But if A were true, C would be amatter of course,
Hence, there is reason to suspectthat A is true.
A Third Type of Inference is Often Recognized
While abduction was recognized by Aristotle, it was not until
the 19th century thatthe importance of this type of reasoning was
recognized. The most prominentproponent to study the relations of
abduction to deduction and induction wasCharles Sanders Peirce
(pronounced 'Purse'). But, it was not until the second half ofthe
20th century that philosophers and scientists started to take
seriously theimportance of abduction.
-
Rule: All marbles in this bag [M] are red [P].
Abduction
A Simple Example
In abduction, the major premise is the Rule.
-
Rule: All marbles in this bag [M] are red [P].
Result: This marble [S] is red [P].
Abduction
A Simple Example
The minor premise is the Result. Notice that the predicate,
'red,' appears in bothpremises.
-
Rule: All marbles in this bag [M] are red [P].
Result: This marble [S] is red [P].
Case: This marble [S] is from this bag [M & P].
Abduction
A Simple Example
What you should notice is that the Rule, as a theory, is applied
to the Result, wherethe Result can be regarded as an effect. The
conclusion, Case, then has the qualityof an explanatory account. In
this example, we explain why 'this marble' is redbecause it came
from 'this bag' of red marbles.
-
Rule: All marbles in this bag [M] are red [P].
Result: This marble [S] is red [P].
Case: This marble [S] is from this bag [M].
Abduction
A Simple Example
TRUE
TRUE
TRUE / FALSE
As with any non-deductive inference, the true premises of an
abduction do notguarantee the truth of the conclusion.
-
P
M S
P
M S
Rule: The marbles in this bag [M]are red [P].
Result: This marble [S] is red [P].
Case: This marble [S] is from this bag [M].
exclusion
Abduction
(a) (b)
The structure of abductive inference is the conjunction of some
theory or law-likestatement (Rule) and observed effects (Result) to
conclude a possible cause (Case).Abduction is sometimes referred to
as 'reverse deduction' in that the Case (cause) isconcluded from
the Rule (theory) and Result (effect), rather than the Result
beingconcluded from the Rule and Case as in deduction.
As a result (a), it is the presence of the predicate (P) in both
premises whichsuggests the relation between the subject (S) and
middle term (M) in theconclusion. Unlike deduction, which shows
'inclusion,' and induction, which shows'partial inclusion,'
abduction is characterized by 'exclusion' (b).
-
Induction & Abduction
Ampliative: conclusion can imply thingsnot stated in
premises.
Not necessarily truth preserving: truthof conclusion not
guaranteed.
Support for conclusion by premises canvary in strength.
Requirement of total evidence must beconsidered.
Deduction
Not ampliative: conclusion cannot gobeyond what is stated in
premises.
Truth preserving: conclusion is true ifpremises are true.
Degree of support for conclusionirrelevant - conclusion is
either true orfalse.
Requirement of total evidence issatisfied automatically.
Relations Between Non-Deductiveand Deductive Inference
There are some fundamental distinctions we need to be aware of
between deductiveand non-deductive (induction & abduction)
reasoning. As we will see, thesecharacteristics are significantly
important when examining the types of reasoningused in biological
systematics.
-
AMPLIATIVE REASONING
Requirements
C Non-monotonic: allow a certain conclusion to be defeatedby
inclusion of additional information inpremises.
C Cut-off Point Problem: show that generalizations
fromobservations are justified.
C Vertical Extrapolation: support conclusions that make
referenceto entities not referred to in premises.
C Eliminative Dimension: allow multiple conclusions consistent
withpremises.
Since non-deductive reasoning is ampliative (see previous
slide), there are fourcharacteristics that need to be
recognized.
-
C Non-monotonic: allow a certain conclusion to be defeatedby
inclusion of additional information inpremises.
C Cut-off Point Problem: show that generalizations from
observationsare justified.
C Vertical Extrapolation: support conclusions that make
reference toentities not referred to in premises.
C Eliminative Dimension: allow multiple conclusions consistent
withpremises.
Induction
Induction / Abduction
Induction / Abduction
Induction / Abduction
AMPLIATIVE REASONING
Requirements
Most of these characteristics apply to both induction and
abduction.
-
The Philosophy of Biological Systematics
Course Outline Part 1
1. The goal of Science. The goal of biological systematics.
2. Causal relationships in systematics.
3. The nature of why-questions.
4. The three forms of inference: deduction, induction,
abduction.
5. The uses of deduction, induction, and abduction in
science.
We are now in a position to examine the specific ways in which
deduction,induction, and abduction are used in our processes of
scientific inquiry.
-
Inferences in Science
-
hypothesish
datad
deduction
(1) Deduction: predictions of potential test consequencesderived
from the hypothesis to be tested.
Deduction & Induction
induction
h
(2) Induction: performing the test; observations of
testconsequences, providing either confirming/corroborating or
disconfirming/falsifyingevidence.
deduction induction
h
d
The Popular View of Their Relations
Recall that earlier we noted that people often speak of the
relations of deductionand induction in science, where science is
only seen as cycles of deduction andinduction in a continual
process of inferring and evaluating theories/hypotheses.
But in fact, abduction is a fundamental component that we need
to take intoconsideration as completely separate from induction
(sensu stricto).
-
Operational Relations BetweenTypes of Inference in Science
deduction
abduction
induction
Inferences ofHypotheses & Theories
Inferences of Tests
Conducting Tests:Hypothesis Acceptance or Rejection
The actual relations between abduction, deduction, and induction
are summarizedhere. Abduction involves our reasoning process for
inferring hypotheses andtheories. Deduction is used to derive
potential consequences from our hypothesesand theories that might
serve as test evidence when the act of testing occurs.Induction is
the process of testing that leads to our concluding that a theory
orhypothesis is confirmed or disconfirmed.
-
Fact
Hypothesis
Theory
What do these terms mean?
In order to clearly understand the different types of reasoning
we use in science,including biological systematics, we need to
first understand the meanings of threewords that are commonly used,
but too often misunderstood.
-
The facts
Facts are objectsand events. Theconditions of truthor falsity do
notapply to facts.
Fact
A 'fact' is nothing more than an object or event that exists,
whether we perceive it ornot. It is important not to confuse the
observation statement, 'This is a glass of icewater,' with the
facts you perceive. The facts exist independent of you.
Yourobservation statement is a conclusion from your inference
(abduction!) used toexplain the facts.
Also, keep in mind that the conditions of truth or falsity
cannot be applied to facts.Facts simply are! What can be true or
false are your statements regarding thosefacts.
-
...a fact is either the being of a thing in a givenstate, or an
event occurring in a thing.
Constructs do not qualify as facts since theyare not objects
that can be in a certain state, letalone undergo changes of
state.... Similarly,there are no 'scientific facts': only a
procedureto attain knowledge can be scientific (or not),not the
object of our investigation. Accordingly,scientists neither
'collect' facts nor do theycome up with or, worse, 'construct'
facts, butadvance hypotheses and theories referring toor
representing facts.
Mahner & Bunge (1997: 34), Foundations ofBiophilosophy
Fact
The quote shown here is an excellent definition of 'fact,' and
corrects a long-standing misconception that we have 'scientific'
facts as opposed to 'non-scientific'facts.
-
Inference of a Theory
Now that we know what facts are, we need to understand the
meaning of the term'theory' and how they are inferred.
-
theories are spatio-temporallyunrestricted.
An explanatory concept(s),stating cause-effect relations,that we
can apply to oursense perceptions, to give usunderstanding.
Theory
theories are not limited to therealm of Science.
What is important to notice in this definition is that a theory
is a spatio-temporallyunrestricted concept. In other words, a
theory can be applied to the past, present,and future. It does not
refer to a specific instance. And, as you will recall that thegoal
of science is to increase our causal understanding, theories are
thefundamentally important conceptual tools that allow us to pursue
thatunderstanding, because theories enable us to infer explanatory
hypotheses.
-
Abductive Inference as theMechanism for Theory Formation
observed effects in need of being explained
background knowledge (theories, laws, etc.)
tentative theory of cause-effect relations(adapted from an
analogous theory)
explanatory hypothesis
The inference of a theory is by way of abduction, and often as a
matter of analogy.One takes a previously established theory, and
uses it as an analogy for a newtheory, where that analogous
application serves to explain some set of surprising orunexpected
phenomena.
-
Observations:
There are differentially shared traits among these observed
organisms.
variation / inheritance / differential survival and
reproduction
Background knowledge:
Based on what is known of the actions of artificial selection,
in con-junction with the above background knowledge, maybe an
analogoussystem of cause and effect relations exists in nature:
Tentative theory:
Abductive Inference as the Mechanismfor Theory Formation
Natural selection - organisms with traits that enhance survival
andreproduction will leave offspring with those traits .
Variation arose in an ancestral population, subsequent to which
thetraits in question allowed for enhanced survival and
reproduction.
Hypothesis:
A classic example of the combined use of analogy and abductive
inference can befound in the development of Charles Darwin's (1859)
theory of natural selection.
-
Inference of a Hypothesis
-
An explanation of someset of facts, giving us atleast initial
understandingof what we perceive.
hypotheses are not limited to therealm of Science.
Hypothesis
hypotheses are spatio-temporallyrestricted.
Notice that unlike a theory, which does not refer to specific
instances, a hypothesisdoes present a narrow set of conditions for
a particular time and location. In thecontext of science, the most
useful way to characterize hypotheses is as explanatoryaccounts,
the purpose of which is to provide us with causal understanding of
anobserved effect or set of effects.
-
Abductive Inference of a Hypothesis
observed effects in need of being explained
theory (cause-effect relations)
explanatory hypothesis
background knowledge
The schematic example shown here illustrates the most basic
components of theabductive inference of a hypothesis. The premises
comprise at least one theory thatis applied to the effect(s) we
wish to explain, from which we conclude anexplanatory hypothesis
that suggests that the effect(s) is/are the product ofparticular
past causal events that are consistent with the theory.
-
The inferential process of critical-ly and empirically assessing
theability of theories and hypothesesto give us understanding.
TESTING: a definition
Now that we have examined the basics of inference, including the
inferences ofhypotheses and theories by way of abduction, we can
briefly look at the process oftesting. We will address testing in
greater detail later in the course, as it applies tothe testing of
biological systematics hypotheses.
-
Present(the realm of Observation)
Past Future
Cause
Effect
predictionEffect
ExperimentalSciences
abductionExplanatoryHypothesis
HistoricalSciences
The Two Realms of Science
Hypothesis testing Theory testing
Recall the distinction we made earlier between 'historical' and
'experimental'sciences. This will serve to illustrate the
difference between the testing ofhypotheses and theories.
-
Present(the realm of Observation)
Known Cause(experiment)
EXPERIMENTAL
Future
Effect (potentiallyobservable)prediction
(deduction via theory)
HISTORICAL
KnownEffect
Past
Unknown Cause(not observable) explanation
Testing: Experimental vs.Historical Sciences
Hypothesis testing Theory testing
While the focus of this course will be on explanatory hypotheses
in the historicalsciences, most discussions about testing use
examples from the experimentalsciences. There are some important
differences between these fields regarding thenature of testing,
that need to be mentioned. What is of principle interest in
theexperimental sciences is testing by way of controlled
experiments.
A theory is tested by providing controlled (e.g. experimental)
causal conditions inthe present. In other words, the causal
conditions are known to us. It is then a matterof observing whether
or not a predicted effect occurs. What you will notice is thatboth
cause and effect can be observed. We have the opportunity to know
both.
But, in the case of the historical sciences, what we know in the
present are effectsthat are in need of being explained. The
difficulty is that the cause that explainsobserved effects occurred
in the past so no longer exists in the present. As a result,the
cause is often unknown and unobservable.
-
Present(the realm of Observation)
Known Cause(experiment)
EXPERIMENTAL
Future
Effect (potentiallyobservable)prediction
(deduction via theory)
HISTORICAL
KnownEffect
Past
explanation
ExplanatoryHypothesis
Hypothesis testing Theory testing
Testing: Experimental vs.Historical Sciences
Thus, we infer an explanatory hypothesis to account for the
observed effects. It isthis hypothesis that we then want to test.
But, in comparison to the experimentalsciences, where the relations
between cause and effect can both be known, the factthat a past
causal event is usually not known can make it very difficult to
testexplanatory hypotheses since the relevant effects needed for a
test might not beavailable. We will see in this course that this
limitation certainly applies to thetesting of many biological
systematics hypotheses.
-
KnownEffect
Present(the realm of Observation)
Past
abduction
ExplanatoryHypothesis
Specific CausalCondition(s)
test that shouldbe performed
deduction
Future
testing of hypothesis byobservations of effects
induction
Testing Explanatory Hypotheses
We can now summarize the relations between the abductive
inference of anexplanatory hypothesis and the subsequent testing of
that hypothesis.
It is from effects observed in the present that we infer by way
of abduction anexplanatory hypothesis. From the specific causal
conditions stated in thathypothesis we deduce effects that should
be observed that are only possible becausethe specified causal
conditions that occurred in the past would allow for thoseeffects.
The deduction of such effects provides the basis for the tests that
need to beperformed.
The act of testing the hypothesis is, however, a matter of
induction, where thehypothesis is either accepted or rejected on
the basis of searching for the specifiedtest evidence. Since no
test can guarantee the truth of a hypothesis, and adisconfirmed
hypothesis simply leaves us with alternative hypotheses to
consider,testing is always inductive.
-
Observed Effects
Why...?
background knowledge+ causal theory
Abduction:causal theory + observed effects
Hypotheses
I. ABDUCTION
The Inference of Hypotheses
Let's now look a very simple summary of the relations between
abduction,deduction, and induction. In this slide, the abductive
inference of hypotheses ispresented.
-
AdditionalEffects
Hypotheses
The Inference of New Hypotheses:additional abductive inferences
are required when new effects are observed
II. ABDUCTION
Very often, subsequent to inferring a hypothesis (or
hypotheses), we encounteradditional effects or observations that
also need to be explained in the same manneras the previous
effects.
-
AdditionalEffects
New Set ofObserved Effects(old + new)
Hypotheses
The Inference of New Hypotheses:additional abductive inferences
are required when new effects are observed
II. ABDUCTION
Why...?
The result is that these additional effects/o