Methodology of Scientific Research Programs

Imre Lakatos, 1978

An adequately rational reconstruction of science has to evaluate as scientific not a single theory but instead of it a group of interrelated theories; Lakatos called them scientific research programs, which are composed of a conventionally accepted ‘hard core’ of interacting theories and a ‘belt’ of protective auxiliary hypotheses, and proposed the sophisticated falsationism as a criterion to select between rival programs. I agree with that methodology and I am going to present some reasons to support this position.

First at all, the statements which are inconsistent with the program can not defeat it. The program has a heuristic that allows us to save the program: we modify the belt without changing the hardcore; in this way, we can always reconcile the theories and the factual propositions. With sufficient resourcefulness and some luck, we can defend any program for a long time, even if it is false. Mere ‘falsifications’ must not imply rejection; they are to be considered –to convert them in corroborating examples- but need not be acted upon. The pattern of trial –by hypothesis- and error –shown by experiment-, is to be abandoned because no experiment is crucial to defeat a program.

Due to the fact that a program can not be defeated by the anomalies, the only way to decide when to abandon a program is the construction of a better one, which means that it has an excess empirical content over its predecessors, some of which is subsequently verified. As a consequence of this we have rival programs. If a program explains more than the rival, the latter will be falsified; therefore, the falsationism –a sophisticated one- requires competing programs. The competition is significant and leads to a rational reconstruction of scientific change in which each rival try to increase its content and predict novel facts. On the other hand, no advantage for one side can ever be regarded as absolutely conclusive; a novel belt of auxiliary hypotheses can strengthen a program. Consequently, the heuristic allows us to continue working in a program, as a positive outcome of that we won’t reject a program if the anomalies take place, giving us the opportunity to look at the potential of it.

Even though we can modify the belt of auxiliary hypotheses, there is a difference between the scientific modifications and the pseudoscientific ones that we make. A research program is said to be progressing –and therefore scientific- as long as its theoretical growth anticipates its empirical growth, that is, as long as it keeps predicting novel facts with some success. Conversely, a research program is said to be degenerating –and consequently, pseudoscientific- if it gives only a reinterpretation –a linguistic one- of facts anticipated, and discovered in a rival program. According to this methodology the greatest scientific achievement are research programs which can be evaluated in terms of progressive and degenerating problem shifts.

Another fundamental point is that the methodology of scientific research programs has a historical character. If we wan to follow this methodology and develop a scientific program we will look in history for rival research programs and if instead of it we want to explain different speeds of development of different research program we may need to invoke external history. Moreover, the scientific revolutions along the history are shifts of one program over another.

We need a lot of time to evaluate a research program, but this evaluation is stricter because it requires that the belt of auxiliary hypotheses –following a positive heuristic- turn into a progressive shift and predicts novel facts. The methodology of research programs, finally, emphasizes long-extended theoretical and empirical competition of major research programs, progressive and degenerating problem-shifts, and the slowly emerging victory of one program over the other.

The Evolutionary Species Concept

E. O. Wiley and Richard L. Mayden

An evolutionary species is an entity of organisms that maintains its identity from other such entities through time and over space and that has its own independent evolutionary fate and historical tendencies. Species are lineages, ontological individuals existing though time and bounded by speciation events.

The evolutionary species are logical individuals with origins, existence and ends. They are tokogenetic entities that function in the phylogenic system as the analog of phylogenetic entities, clades. Sexual species may show cohesion patterns such that the tokogenetic relationship among the organisms are not well correlated with, or are uncorrelated with, any hierarchical relationships that might exist among those organisms. On the other hand, asexual species have tokogenetic relationships that are similar to multicellular individual organisms in being composed of tokogenetic clone vectors descended from a single ancestor.

The evolutionary species maintain their identities, which refers to the reestablishment of the tokogenetic network when subsequent sympatry occurs between populations that had been allopatric. Particular species are the result of historical processes and then we have discovered them during the course of our research. They have independent tendencies which imply that they are free to vary and evolve independent of their sister species. They also have an evolutionary fate which means that the species are real entities and not a result of our imagination; their fate is to speciate or eventually goes extinct.

If the monophyletic groups have objective reality through time, the ancestral lineage and all descendants of that lineage also must have objective reality. The fact that we can reconstruct much of the phylogenetic histories of groups constitutes evidence that independently evolving lineages exist in nature. Another proof that such lineages do exist is derived from the fact that phylogenetic analysis becomes complicated when lineage independence is not strictly maintained.

The evolutionary species concept is the logical analog of the concept of the monophyletic group, therefore it is a strictly genealogical and non-operational concept. Lastly, all evolutionary species are comparable because they are the largest tokogenetic biological system, consequently general phenomena associated with speciation can be studied even among non-sister species.

The phylogenetic Species Concept (sensu Mishler and Thriot): Monophyly, Apomorphy, and Phylogenetic Species Concepts.

Brent D. Mishler and Edward C. Theriot.

A species is the least inclusive taxon recognized in a formal phylogenetic classification. As with all hierarchical level of taxa in such a classification organisms are grouped into species because of evidence of monophyly. Taxa are ranked as species rather than at some higher level because they are the smallest monophyletic groups deemed worthy of formal recognition, because of the amount of support for their monophyly and/or because of their importance in biological process operating on the lineage in question

Sensu Mishler and Theriot, there is no species problem per se in systematics. Rather, there is a taxon problem. Once one has decided what taxon names are to represent in general, then species taxa should be the same kinds of things, just the least inclusive. Evolution is real, as are organisms (physiological units), lineages (phylogenetic units), and demes (interbreeding units), for example. On the other hand, our classification systems are obviously human constructs, meant to serve certain purposes of our own: communication, data storage and retrieval, and predictivity. These purposes are best served by classification systems that reflect our best understanding of natural processes of evolution, and the field of systematics in general has settled on restricting the use of formal taxonomic names to represent phylogenetically natural, monophyletic groups.

A phylogenetic systematic study of a previously unknown group of organisms involves three major temporal, logical phases:

1. In the precladistic phase the elements of a cladistic data matrix are assembled. These elements include OTUs (operational taxonomic units), characters, and character states. OTUs are assembled initially from grouping together of individual specimens that are homogeneous for the characters then known. Here is important to stress that there is no obvious, theory-free way to individuate species. The process must involve analysis, and that analysis must be explicitly phylogenetic.

2. Cladistic analysis involves translation of the data matrix into a cladogram. Reciprocal illumination is often involved here as well because incongruence between characters or odd behaviour of particular OTUs may lead to a return to phase 1, a re-examination of OTUs and characters, primarily to check for fit to the assumptions of the cladistic method.

3. Classifications based on an assessment of the relative support for different clades provide a basis for evolutionary studies. Formal taxa (including species) are named here on the basis of clear support for their existence as monophyletic cross sections of a lineage and for their utility in developing and discussing theories.

Any cladistic analysis that fails to take into account the possibility of reticulation may not be realistic. Not all lineages may have evolved apomorphic characteristics, and so they may not be identifiable through character analysis. That is, there may be monophyletic groups for which there is no direct evidence. This is a general problem for cladistic analysis and is not special to the species problem.

Henninian species concept

Modified Hennigian species concept:

A species concept based on the criterion of "reproductive community" alone does not satisfy the demands of strict phylogenetic systematics (Hennig, 1950 against Mayr). Hennig includes the cohesion (gene flow) to define species. The initial concept of Hennig was revitalized by Willmann (1985; 1986).

Definition:

The modified Hennigian species concept based on reproductive isolation and cohesion through gene flow, because he was interested in the delimitation of species in time (1966). someone support the importance of the cohesion in the delimitation of species; others support the reproductive isolation (Mayr, 1957). The cohesion and reproductive isolation can be applied to the "most inclusive Mendelian population"; but the factor more important is the isolation (reproductive gap).

Agamotaxa are taxa consisting of uniparental organisms originate in a way similar to bisexual species, each agamotaxa is isolated reproductively from all others. The phylogenetics relationships of agamotaxas are different to bisexual populations, the terminals would be organisms individual.

Phylogenetic Justification:

A concept appropriate for phylogenetic systematics must consider the historical dimension of species. The monophyletic groups consist of a stem species and all their descendants (Hennig). Species is viewed as a temporal series of populations connecting two speciation events. If we assume monophyly in the Hennigian concept; we assume that the stem species cannot survive speciation, and a species comprise the entire branch segment between two speciation events.

Species Recognition:

A species concept based on reproductive isolation attempts to describe natural entities (Willmann, 1991). The BSC (Biological species concept) and HSC (Hennigian species concept) is not character related and they is identical if absolute isolation is adopted. In allopatric populations, the breeding experiments in a artificial environment determines whether it belong to the same species (Wiley, 1981). the species concepts based on characters does not inferring species boundaries.

Potential and Actual Interbreeding:

The potentiality of interbreeding of the populations is a important factor for the stability of the BSC. However; the HSC modified (Willmann) only is related to reproductive isolation.

Discussion:

The criterion of absolute isolation is not exclude any arbitrariness (Key, 1981; Willmann, 1985). The use from several criteria can be incorrect. The isolation criterion does not interfere with any kind of biological research.

Survival of the Stem Species:

The populations becomes species only relative to their next kin. Speciation creates a pair of news species, and it eliminate the stem species (Willmann, 1989). If we does not assume the dissolution of the stem species, we does denies that species have boundaries in time.

Biological Species Concept

Ernst Mayr


The Biological Species Concept can be stated as: biological species are groups of interbreeding natural populations that are reproductively isolated from other such groups.

The Biological Species Concept answers the Darwinian Why question, Why are there species? Why do we not find in nature simply an unbroken continuum of similar or more widely diverging organism? An organization of the diversity of life into species permits the protection of harmonious, well balanced, well adapted gene pools, an indiscriminate interbreeding of individuals, would lead to an immediate breakdown of these harmonious genotypes, for this reason the concept is not applicable to organisms that don't form sexual populations, their genotype does not require any protection because it is not threatened by destruction through out crossing.

By what devices is the integrity of a species being maintained? Dobzhansky introduced the term isolating mechanisms for these devices defining them as agents that hinder the interbreeding of groups of individuals or reduces to zero the frequency of exchange of genes between the groups. There is a enormous diversity of such devices : sterility genes, chromosomal incompatibilities, ecological exclusion, behavioral properties that facilitate the recognition of conspecifics.

What a biologist encounters in nature are populations of organism, the task is to assign these populations to species. This requires two operations a.) to develop a concept of what a species is, resulting in the definition of the species category in the Linnean hierarchy an b.) to apply this concept when combining populations into species taxa.

The species taxon refers to a concrete zoological or botanical object consisting of a classifiable population of organism. They are particulars, individuals or biopopulations they can be described and delimited against other species taxa.

The species category indicates a rank in the Linnaean hierarchy, it articulates the concept of the biological species and is defined by the species definition.

Is the species a class or an individual? "The species taxon -any species taxon- is an individual with any member of that particular species being a part of the species. The species category however is a class. It is the class, the species of wich are the species taxa. "(Mayr, 1976)

The criticisms of the Biological Species Concept are directed against the decisitions made in the delimitation of species taxa, in contiguous interbreeding populations it causes no difficulties. However, the criterion of interbreeding would seem to be inapplicable in the delimitation of species wherever isolated populations are involved, populations isolated either in time or space. The basic difficult is that populations isolated evolve as independent gene pools and some of them are on their way to becoming a new species or are actually have passed this threshold. But we must take an inference on the basis of all available data and criteria( analysis of their genetics, molecular biology tools, nature of their isolation mechanism ) as to how far along they have proceed on the way to becoming a separate species. However in most ambiguous situations it is useful to treat allopatric populations of doubtful rank as subspecies , trinomials provide information of closest relationship and allopatry, In ornithology the convention has developed to call strongly differentiated allopatric populations, allospecies.

The biological species concept deal with the definition of the species category , and only has meaning where a gene pool comes into contact with gene pools of other species that is at a given locality and at a given time (the nondimensional situation), However, because species taxa have an extension in space, the species status of noncontiguous populations must be determined by inference. Also species taxa have an extension in time, thus evolving is not such a species criterion, species do not differ in this respect from other living entities.

Defensa a Popper

‘Science does not aim, primarily, at high probabilities. It aims at a high informative content, well backed by experience. But a hypothesis may be probable simply because it tells us nothing, or very little’ (Popper, 1954).

The inductivism is a logic impossible, just because from observational facts, can not being infer theories. The theories are product of a mental process in which we conjecture about reality. Additionally, is technically impossible to observe the entire Phenomena’s events, because is preferable to look for those events (tests) that falsify the theory.

Popper proposed that the truth content of the theories, even the best of them, cannot be verified by scientific testing, but can only be falsified or corroborated. The knowledge is the result of conjectures (response to a given problem situation) which are systematically subjected to the most rigorous attempts at falsification possible. The conjectures that pass the process of refutation are not more true, but rather, more corroborated and then more applicable to the problem situation at hand. This applicability does not predict continued corroboration; neither does rigorous testing protect a conjecture from refutation in the future. So we can never know in fact when something is true, neither from experience, nor from any other source; we only could be sure about is false.

Popper proposed his formula [C(h,e,b) = p(e,hb)-p(e,b)] as a way to explain in a brief and simple way his science philosophy. The two extremes (1, -1) are unattainable, just because we need that the evidence be probable in some way, and because we can never reach the truth (or be sure we reach it). If we got any number above 0, we corroborate our theory, so what the famous 0.5 lets us is to differentiate between naïve and strong falsationism. From the idea at the beginning, we can say that a naïve test is the one, which does not explain more than the trivial.

If we assume that what is called ‘scientific knowledge’ consists only of guesses or conjectures, then this assumption is sufficient for solving the problem of induction, without sacrificing empiricism; that is to say, without adopting a principle of induction and ascribing to it a priori validity. For guesses are not induced from observations (although they may, of course, be suggested to us by observations.) The key to the solution of inductions problem is the recognition that our theories, even the most important ones, and even those which are actually true, always remain conjectures. And the main points given by Popper to solve inductions problem are:

- Acceptance of the view that theories are of supreme importance
- Acceptance of Hume’s argument against induction: any hope that we may posses positive reasons for believing in our theories is destroyed by that argument
- Acceptance of the principle of empiricism scientific theories are rejected or adopted (tentatively) in the light of the results of experimental or observational tests
- Acceptance of critical rationalism: scientific theories are rejected or adopted as being better or worse than other known theories in the light of the results of rational criticism.

All this steer us to a central point in Popper’s philosophy, the problem of demarcation; and sum we can say that a method of looking for verifications, it’s a typical method of a pseudoscience, and it is clearly different and distinguishable from the method of testing a theory as severely as we can – that is, the method of criticism, the method of looking for falsifying instances.

Testability

Elliott Sober
Proceedings and Addresses of the American Philosophical Association, Vol. 73, No. 2. (Nov.,
1999), pp. 47-76.

Nowadays, there is general agreement about the importance of understanding what it takes for a statement to be confirmed or disconfirmed by an observation. There is also a wide consensus that the design of experiments is an important issue; if somebody wants to test a proposition, it is important to make sure that the experiment that is carried out, actually bear on the proposition in question.

Testing is an inherently contrastive activity; and testing a hypothesis requires that it make a prediction that can be checked by observation. We make observations in order to learn about things that we do not observe; these observations must be “theory neutral”, they should be neutral, relative to the competing theories under test.

An empirically soluble problem is one in which the competing hypotheses make different observational predictions. The hypotheses rarely make observational predictions on their own; they require supplementation by auxiliary assumptions if they are to be tested. The problem here is that usually the auxiliary assumptions are looked for, or chosen because the researcher has good reasons to think they are true. This means that the auxiliary assumptions used in a test and the hypotheses under test differ in their epistemological standing. The observational outcomes favour one competing hypothesis over the others. But the test typically will not test the auxiliary assumptions at all. Typically, the auxiliary assumptions are epistemically independent to the test outcome.

Somebody could think that auxiliary assumptions may include idealizations. Nevertheless what is essential is not that one be able to say that a set of assumption is true, but that it is harmless- that correcting the idealization could not affect the conclusion one draws. However, it is not enough just to assert that the idealization is harmless; one must have evidence that this is so.

Finally the author talks about the probability of the hypotheses, and tells us that there is no probabilistic analog of modus tollens. If a hypothesis deductively entails something false, then the hypothesis is false. But if a hypothesis that what you observe was very improbable, what then? It does not follow that the hypothesis it self is improbable. So based on this, we can judge which hypotheses do better and which do worse in their competition, that is all.