Didn't we discuss this before?

I once walked into my colleague's room and pointed out that his sink was leaking and getting some boxes full of reprints wet. I suggested he should get it fixed or move the boxes. We discussed it a little and after a short while it was forgotten. A year later I noticed that the problem had not been fixed. The reprints were all moldy and the leak had spread staining his carpet. I pointed it out to him again. He simply dismissed it with the line "Didn't we discuss this before?"

That same line is used throughout systematics and biogeography to dismiss lengthy heated debates that never were resolved. Who, for instance, were the victors in the following debates?

Cladistics versus Phenetics

Pattern Cladistics versus Numerical cladistics

Modern Synthesis versus Cladistic Revolution

Dispersal versus vicariance

It is said that history is written by the victors. Looking at the above examples we assume that cladistics triumphed over phenetics (overall similarity); Pattern cladistics simply lost a pointless debate; The Modern Synthesis was expelled from numerical revolution and that the dispersalist have finally won in their campaign against the dusty old vicariance biogeographers. In every case above, a heated debate occurred, the problems were addressed and everyone went home feeling like something was resolved. If this is the case why is vicariance still the most prominent theory in systematic biogeography? Why does everyone use phenetic methods? Where have all the cladists gone?

None of the above debates were resolved. Phenetists kept doing phenetics. The idea of overall similarity (a non-cladistic idea) swept over all of numerical phylogenetics. The pattern cladistics never left, the Modern Synthesis never died and vicariance was never abandoned. If we are to complain that this was all discussed before, then isn't it because the debate never really ended?

In a recent paper all opposition to DNA Barcoding was dismissed has “... having been controversial” (Lahaye et al. 2008). The paper suggests that by doing DNA Barcoding regardless of its flaws, immunizes it from any criticism. I am sure if another paper is published criticizing barcoding it would be dismissed with that one line "Didn't we discuss this before?" This is the same tactic used by phenetists (overall similarity), Modern Synthesists and Dispersal Biogeographers. It seems that history is not written by the victors, but by those with leaky sinks, a stained carpet and no ambition to do anything about it. But surely "we have discussed this before?"

References

Lahaye, R., van der Bank, M. Bogarin, D., Warner, J, Pupulin, F., Gigot, G., Maurin, O.,Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of
biodiversity hotspots. PNAS.10.1073/pnas.070993610395.

Biogeography & Systematics: Call for Papers

Biogeography is a complex discipline, in the sense that it deals with complex processes — of evolution of life in space through time — not directly observable, occurred in the geological past. Biogeographical reconstructions demand precise and complex data — systematic and distributional information — and intricate methods. It should be no surprise to learn that evolutionary biogeography is a relatively recent area of research within the history of comparative biology.

The late 1970s and early 1980s faced an especially rich period of development of biogeographical theory and methodology, with the inclusion of the concept of vicariance in the mainstream of biological literature. The journal Systematic Zoology played a major role in the publication of papers in this area during that period. The intricacies of the subject, however, along with decisions concerning the policies of the primary main journals of the subject — Systematic Biology, Cladistics and Journal of Biogeography — resulted in problems publishing large papers with analytical studies of historical biogeography. Typically large papers with biogeographical studies also contain analyzes of the relationships of a group of organisms, often requiring new taxa to be named, to properly identify the nodes on a cladogram.

To fill this publishing void, the Systematic and Evolutionary Biogeography Association (SEBA) has decided to launch a new, open-access online journal, Biogeography and Systematics, to occupy such niche in the primary literature.

Biogeography & Systematics will publish original papers on historical biogeography and phylogenetic systematics. The journal will have the following sections:

Invited Papers — for topics of major interest in biogeography and systematics under invitation from the editor-in-chief;
Original articles – on analytical, historical, epistemological, and methodological aspects of biogeography and systematics, without page limit;
Forum – opinion pieces on any topic of biogeography or systematics (maximum, 3000 words).
Book Reviews – usually under invitation, but submitted reviews (including classical works) may be considered (max. limit 1000 words).

The editorial policy of Biogeography & Systematics is to ensure that articles published are of the highest quality and relevant to the interests of our readers. The journal is peer-reviewed. The journal is not biased towards any biogeographic region, in terms of taxa studied or author affiliation, nor any method of analysis. All papers shall be written in English (US spelling).

The first number of the journal is scheduled for August, 2008.

Please click here to see the Guide for Authors.

Editorial Policy
Biogeography & Systematics has an editorial policy in order to ensure that the articles we receive are of high quality and relevant to the interests of our readers.

• Biogeography & Systematics publishes in English (US spelling) only.


• Biogeography & Systematics publishes original research papers in biogeography and systematics.


• Biogeography & Systematics is a peer-reviewed journal.


• Biogeography & Systematics publishes monographic taxonomic, systematic and biogeographical treatments.


• Articles may cover any aspect of biogeography, systematics or taxonomy.

Types of Articles
Biogeography & Systematics publishes the following types of articles:

• Biogeographical anaylses, revision of methods or epistomological reviews.


• Systematic revisions that may include biogeographical analyzes.


• Taxonomic treatments that include systematic analyzes.


• Historical revisions in biogeography, systematics and taxonomy, including biographies.

If you have been invited to contribute an article please submit your manuscript as an .odt, .rtf or .doc. We ask authors to only use Primary (bold) headings.

Citations
All citations are to be made without using commas between author and year (Wallace 1855) and commas between multiple authors (e.g. Nelson and Platnick 1981, Brandon-Jones 1998). Quotes should be cited as (Willis 1922, p. 100). Please refer to this issue for further usage of figures (see figure 1 or Fig. 1), tables and numerals.

References
Please include the full titles of journals and books. Do not use abbreviations! Please keep your references in the styles listed below.

Brandon-Jones D. 1998. Pre-glacial Bornean primate impoverishment and Wallace’s line. In Hall R, Holloway JD eds. Biogeography and geological evolution of SE Asia. Leiden: Backhuys Publishers, pp. 393-404.

Heads M. 2006. Panbiogeography of Nothofagus (Nothofagaceae): Analysis of the main species massings. Journal of Biogeography 33: 1066-1075. Merriam CH. 1898. Life zones and crop zones of the United States. U.S. Department of Agriculture Division Biological Survey Bulletin 10: 1-79.

Nelson G, Platnick NI. 1981. Systematics and biogeography: Cladistics and vicariance. New York: Columbia University Press.

Wallace AR. 1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History 16 (2nd series): 184-196. [http://www.victorianweb.org/science/science_texts/wallace_law.html; http://www.wku.edu/~smithch/wallace/S020.htm; http://www.zoo.uib.no/classics/new_species.txt].

Proofs
Authors will be given a chance to proof their paper prior to publication. The final proof will be published on the SEBA website simultaneously as the journal is printed.

Copyright Form
Authors will be asked to complete a copyright form upon acceptance of their manuscript.

Submissions
Please submit your articles in electronic format to the Editor-in-Chief, Dalton de Sousa Amorim

Biogeography & Systematics is printed by the Instituto Venezolano de Investigaciones Científicas, Venezuela.

Defining Phenetics, Intentions and Mimics

Many reading this blog are probably wondering why we seem to call everything phenetics. Phenetics is a term used, incorrectly, to only describe a certain type of methodology, namely clustering based on similarity (i.e., neighbor-joining etc.). In fact phenetics is nothing more than Numerical Taxonomy (Sneath & Sokal, 1973), a topic that we have discussed in a previous blog (Phenetic "Natural" Classifications).

Phenetics attempts to classify organisms based on over-all similarity. An excellent definition of phenetics, which can be found at Wikipedia, goes one step further:

"In biology, phenetics, also known as numerical taxonomy, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation".

Where phenetics becomes problematic is when these classifications are considered to be natural, that is monophyletic. A monophyletic taxon is based on relationship, namely homology. Homology is not a measurement of similarity but an expression of relationship. Phenetically grouped organisms may not necessarily be more closely related to each other than they are to another group. In other words, phenetics cannot distinguish paraphyly from monophyly. An analogous problem exists in biogeography.

Parsimony Anaylsis of Endemicity (PAE) is a method developed in order find similarities between areas (see Rosen 1988). The method simply requires a data matrix of presence and absences of taxic distributions. In contrast, cladistic biogeography demands that taxa used in analysis are monophyletic, however many fossil groups have no relations that coexisted in the same period. This means that some paleontologists are forced to deal with higher taxon biogeography (i.e. at family or ordinal level) or abandon cladistic biogeography altogether. The idea behind PAE is to use any group within a phenetic context. Monophyly is not a requirement of PAE therefore absences can be used to cluster organisms into areas since no notion of homology or relationship is assumed. As with phenetic findings in systematics, some users have made the mistake of assuming that PAE can find phylogenetic signals based on non-evolutionary data, that is, non-homologous information, in the data matrix.

On closer examination we find that many systematists and biogeographers intent on discovering homology, monophyly and endemism are nevertheless using phenetic methods. Perhaps this is due to a lack of readily available methods in the literature. After all, cladistics and cladistic biogeography started off as "pen and paper" methods whereas phenetics was always a numerical method (hence numerical taxonomy). The issue at stake is whether using phenetic methods jeopardizes our intent, namely to search for homologies, monophyly and endemic areas. We argue that it does.

The problems lie in transposing data into a data matrix using neighbor-joining, clustering, parsimony or compatibility as are all phenetic - that is, methods that use overall similarity in order to find classifications. These methods can not distinguish natural (monophyletic) from artificial (non-monophyletic) classifications.

Our favorite programs are rightly pointed out as black-boxes yet we shrug this off and cite Farris (1983) or recite some algorithm. In some extreme cases we justify our intentions by making sure that our data is compatible to our methods (sensu Patterson 1982). But we cannot continue skirting this issue. Similarity is an anathema that our forebears, Goethe, Vic D'Azyr, Saint Hilaire, Owen, the founders of homology had quickly disposed. Similarity is the foundation of phenetics, not cladistics. Our intent to find homology, monophlyly and endemicity (rather than the superficial cousin, similarity) must be held when selecting methods and programs that we use, ne c'est pas?

Assumptions held so dearly by some cladists, such as Patterson's test for homology and similarity as a requisite for monophyly, are all phony. Cladists should not use phenetic methods in order to make sense of classification, instead they should use homology and relationships. The only way (if any) which we are able to use phenetics meaningfully is to treat it as a mimic of the real thing (cladistic pen and paper methods). After all that is what phenetics is about, mimicking reality.

A mimic in cladistics is any phenetic method that attempts to implement a genuine theory or intention. Any phenetic implementation needs to be considered carefully since they were originally not intended for cladistic for biogeographical analysis. Many of the methods and implementations we use today have existed in statistical and mathematical classifications (i.e., data matrix, parsimony, compatibility, clustering, subtrees etc.). Rather than accepting these methods wholeheartedly as being "cladistic", cladists should fool the mimics. This has been successfully done by a program called TAX (Nelson & Ladiges, 1991). TAX fools the program into treating areas of no relationships as questions marks, without treating absences as evidence.

If cladistics is to survive as an evolutionary field intent on finding homologies and monophyly, it needs to re-examine the phenetic methods that it uses. A field that is becoming dependent on phenetic methdology can easily become phenetic.

The image above was made by David Maddison in 1981 when "... Cladistics versus Phenetics debates were still fresh in people's minds". We hope that the same image may re-spark some of that debate. The image may be found on his website.

References

Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 1-47 in Advances in Cladistics, Volume 2, Proceedings of the Second Meeting of the Willi Hennig Society. ed. Norman I. Platnick and V. A. Funk. Columbia University Press, New York.
Nelson, G., & Ladgies, P.Y. 1992. TAS and TAX: MSDOS programs for cladistics, version 3.0. Pub- lished by the authors, New York and Melbourne.
Patterson, C. 1982. Morphology characters and homology. In: K. A. Joysey and A. E. Friday (eds.), Problems of Phylogenetic Reconstruction. Systematics Association Special Volume, 21: 21-74.
Rosen, B.R. (1988) From fossils to Earth history: applied historical biogeography. Analytical biogeography: an integrated approach to the study of animal and plant distributions (ed. by A.A. Myers and P.S. Giller), pp. 437–481. Chapman & Hall,
London
Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy — The principles and practice of numerical classification. W. H. Freeman, San Francisco.

Evidence and Motive: Anna's Hummingbird and Loretta's knife

As comparative biologists we are limited in our knowledge of the natural world. We know for instance that some groups are natural and that they share closer relationships with each other than they do to other groups. We also know that some taxa belong to certain groups while others do not. Take the case of Anna's hummingbird (Calypte anna). It is a taxa that belongs to a monophyletic group called birds. We discover that Anna's hummingbird shares closer relationships with other birds than it does to say mammals. As a systematist relationships are all we know of the phylogeny of Anna's hummingbird.

Knowing a relationship doesn't seem to grab the attention of the general public, students or granting bodies as much as evolutionary mechanisms do. What if we proposed that Anna's hummingbird originated in Madagascar and generated a plausible rational argument to support that hypothesis? Suddenly we stir some interest within the biogeographic and marco-ecology communities. When we propose that hummingbirds and birds as a whole are not only related to therapods, but are also their descendants, do we really get everyone excited. But what happens when we reverse the situation - swap our knowledge of hummingbird relationships as explanatory hypotheses and explanatory hypotheses as knowledge? Ebach & Williams (2004) proposed a thinking exercise that is analogous to the suggested proposition above.

Loretta the Murderess

A hypothetical group of detectives kick down a locked door. Behind it stands a woman who answers to the name of Loretta. Next to her on the floor lies a man with a knife in his back. All three objects are covered in blood, which upon further investigation turns out to belong to the deceased. For added effect, the knife has the word "Loretta" inscribed on it in black ink. How do we interpret the scene?

As the title suggests we may call it a "murder", and "a horrible accident", or even "an act of self defense". Whatever the motive is, what is unmistakable is that the locked room contains a woman (Loretta), a man (deceased) and a knife (inscribed with the name "Loretta"). Since no one outside the room witness any action or event, all motives are suspended. All we know are the existence of these three objects.

Let us say that, for some unexplainable reason, the scene is no longer investigated and, for the sake of this argument, all information relating to the Man, the knife and Loretta vanishes. We are left are a series of conflicting motives (i.e., vengeance vs. victimization) and morals (i.e., justice vs. injustice) that all are supported by that same evidence. Now for the analogy - what would happen if we were to swap the evidence for motive and the motive for evidence?

Depending on which way you argue the "evidence" (read "motive") Loretta's innocence is based on the best argument based on the "motive" (read "evidence"). We may propose two explanations to defend or accuse Loretta, namely the "extremely vengeful person" hypothesis and the "victimized person" theory. Each of these totally conflicting theories however based on the same "motive" (read "evidence") - a knife, a dead man and Loretta covered in blood all located in a single locked room. Given that this is all that there is in terms of real evidence, any hypothesis can be made to fit based on nothing more than rhetoric.

Thankfully we no longer live in a society where motives are considered to be evidence (e.g., witch-hunts and other heresies). We do however live in a society that does treat its subjective mechanisms as evidence and its evidence as explanation.

There would be many people who would support the following argument below:

"Birds have evolved from Dinosaurs"

or

"The center of origin for hominids is Africa"

Let us take the first argument. The motive or explanation has been replaced as "evidence". Birds have not evolved from Dinosaurs because "Dinosuars" do not exist as an evolutionary group, that is a monophyletic or natural group. The Dinosauria as a non-monophyletic group is real evidence. The argument that Dinosaurs evolved into birds is by far a more exciting prospect. In doing so however we disregard the evidence to hand - namely that Dinosaurs are a non-evolutionary grouping. The second argument is similar.

We as outside observers have never seen Loretta place the knife into the man, we assume she did because it is her knife and the room was locked. Guilt by association is a terrible tragedy when it occurs in our legal system, but the practice is encouraged in systematics and biogeography. The oldest hominid remains are found in Africa, therefore it is assumed that this is where the group originated from. Guilt by association is not empirical or scientific in anyway as it is based mere speculation, namely what may or may not be there. Additionally no one has seen hominids originate in Africa, so the whole argument is superfluous and speculative, every much like the motive (if any) in the Loretta example. If an older hominid bone is found elsewhere, say Antarctica, the hypothesis will change, but be based on motive rather than on evidence. Systematics and biogeography may appear to become more interesting the more non-empirical hypotheses we spout, but by no means do we become more knowledgeable.

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791-794.

Explanations and Bad Science

Explanations are wonderful things. They provide the world around us with meaning, a way of reasoning with others and a path to understanding scientific processes. Explanations may also sow the seeds of bad science.

Bad Science can be interpreted in a number of ways. The media and “science” journalists interpret “bad” science to mean anti-science or “science” conducted by non-scientists, based on results that are corrupted, forged or spurious. We believe however that bad science is nothing more than “made-up-ology”, which is created by scientists in order to make highly speculative claims to explain natural phenomena. Strangely the media never pick up on our version of bad science, possibly because “science” journalists are there to report positively about science rather than to criticize scientific explanations.

Anyone with enough qualification to report on scientific endeavor has the ability to see through spurious claims, reconstructions or theories. Dinosaur reconstructions based on a single jaw fragments for instance, rate highly in our list of bad science. There are limits to reconstructions, many of which never see the light of day in scientific journals but feature on the cover of “scientific” magazines. The aim of such reconstructions apparently are to to communicate a predicted past event, such a meteorite impact, to a popular audience. The idea is analogous to comparing a period-dress Hollywood blockbuster to an actual historical event. The event most likely occurred, but since it was not recorded in detail nor witness by anyone living, still remains unknown. Discovering a dinosaur jaw or even complete skull does not mean we can determine its size or colour; reconstructions and films based on “true events”, the actual machinations, are fictitious. Reconstructions however are powerful ways to explain important events.

The Power of Explanation

Explanations are mechanical devices with which to predict or retrodict future or past events and processes that are unobservable. Most important is that explanations rely on discoveries.

In experimental science, such as chemistry, phenomena are observable and repeatable. We may discover for instance that two chemicals added together produce another. The event can be repeated, described and observed, therefore resulting in an explanation of the processes involved. Non-experimental sciences such as palaeontology however rely on retrodictions based on evidence to hand. The discovery of a fossil jaw bone for example, is limited to description and observation of its form. The processes that the jaw bone underwent when it was part of a living creature are unobservable and not repeatable. The resulting explanations are quite different from those in chemistry as they are based on assumptions, theories, hypotheses and comparisons. In palaeontology we choose the best explanation based on the most convincing and rational argument. That argument is tied to accepted theories and hypotheses at the time meaning that explanations are forever changing and ephemeral. This does not mean that non-experimental sciences like palaeontology are bad or non-scientific. Many scientific fields that involve the study of past events are far more reliant on patterns than the experimental sciences (i.e., ecology, systematics, biogeography, geology, geography). Explanation, it seems, provides greater meaning.

The non-experimental sciences are primarily descriptive and comparative, relying on form and its relationship rather than on explanations. Given that normal processes are taken for granted in the experimental sciences (i.e. photosynthesis, digestion, ontogeny etc.), they are not evident in the non-experimental fields. Without the luxury of observing processes, scientists are reduced to making up hypothetical explanations in order to provide some kind of meaning. This is understandable in a world where explanations are seen to be more meaningful that form. For us form, its description and comparison, is meaningful. The discovery of patterns and relationships between form is possibly the most powerful scientific endevour. Without it we live in the present with no knowledge of the past. Many scientists within palaeontology, geology, systematics and biogeography feel that the discovery of relationship is not enough. The rise of hypothetical mechanical explanations as “meaningful” is where we believe bad science to begin.

Divisions: Who watches the philosophers of science?

There are a few things for the poor old philosophers of science to get over.

If Peter Lipton is right, namely that,

"Astronomers study the stars; philosophers of science study the astronomers. That is, philosophers of science—along with historians and sociologists of science—are in the business of trying to account for how science works and what it achieves" (Lipton, 2005: 1259).

then philosophers of science have to able to see beyond current trends and political avarice. After all who watches the philosophers of science?

The trend of embracing apparent dichotomies within systematics and biogeography rather than question them, is one of things that philosophers of science need to get over. Philosophers of science need to question, examine and assess such divisions and not blindly accept them as many seem to do.

Below we list the top 10 dichotomies in systematics and biogeography that philosophers of science need to get over:

1. Morphology and Molecules
2. Homology and analogy
3. Homology and homoplasy
4. Transformational and Taxic Homology
5. Synapomorphy and symplesiomorphy
6. Congruence and consensus
7. Cladistics and Phenetics
8. Simultaneous analysis and separate analysis
9. Ecological and Historical Biogeography
10. Dispersal and Vicariance

Just because scientists use these divisions does not mean they actually exist. Dichotomies often groups "us" from "them". Science is not immune from subjectivity or distortion of "the facts" through clever manipulation. Scientific decisions too are sometimes decided upon politics, personality and fashion.

Philosophers of science are there to make sure that fish caught last Sunday afternoon was indeed "that big". In believing, rather than questioning, the divisions between certain ideas that are made by scientists, philosophers of science are unable to for "account for how science works". For some philosophers of science, the one that got away was "ooh .. so big, bigger than anything you have ever seen".

Lipton concludes

"Indeed, one might go so far as to worry that if philosophy did have any impact on scientists, it would be pernicious, depriving them of the kinds of commitment and confidence upon which their practice depends" (Lipton, 2005: 1269).

Philosophers of science have already influenced science, based on some of the highly questionable divisions listed above, to the extent that that it has been fashionable to attribute the cladistics/phenetics "war" in systematics to real events rather than to a poor account of how science functions (i.e., Hull, 1988).

References
Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Lipton, P. 2005. The Medawar Lecture 2004: The truth about science. Philosophical Transactions of the Royal Society of London B, 360, 1259–1269.

Buddah: Look at the moon, not my finger!

Joe Felsenstein has suggested an analytical example, one he felt we might like to examine. The example is simple:

"If we take a sequence alignment, perhaps an easy case such as an alignment of exon sequences of a gene, and then we run (say) a parsimony algorithm, and consider ourselves to be making an estimate of the unrooted evolutionary tree (perhaps later rooting it by outgroup), what do Ebach and Williams say of this?"(Felsenstein in Comments)

Felsenstein kindly offers a few suggestions ("guesses") as to what we might think. These are as follows::

1. It is not inferring the phylogeny because this process is "phenetic"


2. It is not making a classification so it is fine but not of interest to us


3. It should instead be trying to make a classification


4. It is making a classification but a "phenetic" one so not a good one.

Felsenstein offers a view as to which of the suggestions ("guesses") is correct, opting for number 4: 'It is making a classification but a "phenetic" one so not a good one'.

Of course, we welcome helpful suggestions ("guesses"), as our desire has been (and hopefully will remain) the examination of the process of systematics, a complex field that develops and grows, as does all science. Thus, we crave his indulgence at our dissection of his suggestions in the interest of scientific endeavour.

First, we find it a little troublesome to deal with efforts that are thought ‘good’ or "bad" and do not really know what those words might mean in the context above. To us, phenetics is neither good nor bad. Consider the following. Linnaeus created the Sexual System of classification for plants, a system he acknowledged as artificial. That system still has its uses, when one is faced with a particular plant and needs to know its name, then (usually) that can achieved by working through the Sexual System. It is an Artificial Classification – it is neither bad nor good (Linnaeus knew that). It is inappropriate when wishing to investigate the natural system; it is appropriate when wishing to find a name.

Second, whether one is "inferring the phylogeny" or just exploring the distribution of homologies, any branching diagram that results can be made into a classification. Thus, points 1—4 above are without meaning.

In our (several) posts we noted that Natural Classification is investigated using homologies – and similarities, in and of themselves, are not homologies. Consider a matrix of characters, with either 1's and 0's or A's and T's ("…take a sequence alignment…"). What are they? Similarities. The matrix is, one might say, phenetic. The application of UPGMA, or Neighbor-joining, or parsimony, or…well, whatever, cannot change that fact. And, it would appear, that UPGMA, or Neighbor-joining, or parsimony, and so on, are all forms of weighting, regardless of whether one might believe that the 'model' is an accurate representation of the evolutionary process. Now as we noted, "Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic." Thus, we might offer the following: much of the last 40 years of exploration of methods has, inadvertently, focused on ways one might modify or adjust a matrix of similarities.

We do not have, nor do we promote, any "favorite approach…". This is not a competition. Systematics (classification, phylogeny) is about homologies and their distribution.

The cladistic revolution of the 1960s was necessary because of palaeontology, its promises, its claims, and what it delivered. Palaeontology is reformed as a consequence, yet its effect on systematics, mostly detrimental, lasted 100 years.

Perhaps it's time for another revolution.