The phylogeny of plastic bag ties

Some years ago Larisa Lehmer, Bruce Ragsdale, John Daniel, Edwin Hayashi and Robert Kvalstad published a medical report about an ingested plastic bag closure caught in someone's colon (Plastic bag clip discovered in partial colectomy accompanying proposal for phylogenic plastic bag clip classification. BMJ Case Reports 2011). This sounds quite painful.

What is more interesting, though, is that the report was accompanied by a phylogenetic and taxonomic evaluation of plastic ties in general, which the authors named Occlupanids.

Note that the proposed morphological changes in the phylogeny match Cope's Rule of phyletic size increase, as discussed in a previous blog post (Steven Jay Gould was wrong).

Shortly afterwards, one of the authors, John Daniel, set up a web page with a more detailed analysis, under the guise of the Holotypic Occlupanid Research Group (HORG).

Among a lot of other interesting information, there is a revised phylogenetic analysis.

Given the data, it seems fairly clear that the genealogical relationship among these objects is reticulate, and that the trees should thus actually be networks. This follows from the simple fact that these phylogenies are rather uninformative (they are bushes showing a few character transformation series). Also, note that contemporary taxa are ancestors, so that the diagrams are more like population networks than species networks.

These ties are used for packets of sliced bread (a relatively recent invention), and so there has been an explosion of Occlupanid forms as they occupy a new adaptive zone. This is a classic instance of recent speciation that is not yet complete. Occlupanids have now reached pest proportions, except where governments have instituted erradication programmes (such as Europe, where they are no longer found).

Part of the difficulty of analysis is that the objects shown constitute only a small part of the known diversity of Occlupanids (e.g. see this photo and this one). There are a number of manufacturers, and their products constitute separate historical lineages. Morphological features have been transferred from one lineage to another, which is a classic case of reticulate history that has not been taken into account in the above phylogenies.

Indeed, the HORG page is not the only detailed web resource about bread ties — see also the now-defunct but fascinating Transactoid page.

Pierre Trémaux, the unknown phylogeneticist

Pierre Trémaux is a name that most of you will not have heard of, and yet he was a remarkable man. Or, rather, he wrote one remarkable book that has been almost completely ignored by history.

Trémaux (1818-1895) has been described as "a French architect, orientalist and photographer", but in his late 40s he also became a theoretical biologist, and it is this latter context that is of interest here. His best-known book is Origin et Transformations de l'Homme et des Autres Êtres (1865, L. Hachette, Paris). The ambitious nature of this book is indicated by its subtitle: Indiquant la transformation des êtres organisés, la formation des espèces, les conditions qui produisent les types, l'instinct et les facultés intellectuelles, la base des sciences naturelles, historiques, politiques, etc. [Indicating the transformation of organized beings; the formation of species; the conditions that produce the types, the instinct and the intellectual faculties; the base of natural sciences, history, politics, etc.]

In this book the author did four noteworthy and original things regarding phylogenetics:

1. he drew the first "proper" post-Darwinian phylogenetic tree (ie. showing speciation and extinction, with the internal branches as ancestors and the leaves as extant organisms), which connects all of the historical branches back to a single origin (which Darwin's diagram does not show)
2. he discussed the idea that speciation is concentrated at certain times in the geological record (the boundaries between "ages") and that there is effectively evolutionary stasis at other times, which presages Eldredge and Gould's theory of punctuated equilibrium by more than a century
3. he presented the idea that species form in geographically isolated populations, thus beating Moritz Wagner to the idea of allopatric speciation by 3 years
4. he applied Darwinian ideas to the evolution of Homo sapiens, 6 years before Darwin explicitly did so himself. (Thomas Henry Huxley contributed to the topic in 1863, but his book is best known for its infamous frontispiece illustrating transformational evolution among apes.)

Points (1) and (2) are illustrated in the only diagram in Trémaux's book, as reproduced here.

Trémaux's phylogenetic tree (from Google Books)

The text translates as:

Origin and Transformations of Beings

Synoptic figure of the transformation of species, by P. Trémaux

Species of different branches of the animal kingdom, arising from the same origin (the primordial cell or utricle), subdivide age by age; some of the species become extinct in every age, the others continue to grow and to divide and diverge more and more in their characters.

As far as point (1) is concerned, it is important to note that Darwin's 'tree' diagram is not connected to his description of the Tree of Life. The diagram is used to describe his vision of divergence, and descent with modification; at no stage does he refer to it as a "tree". His dry-as-dust description of the diagram and his poetic evocation of the biblical Tree thus have nothing to do with each other. It is merely a modern fancy to suggest that Darwin drew what we would now call a phylogenetic tree.

Therefore, Trémaux seems to have been the first to publish an illustration of the concept of a phylogenetic tree, in the form in which we know it today. St George Mivart, on the other hand, seems to have been the first to publish an empirical phylogenetic tree, in the same year (1865; see Who published the first phylogenetic tree?).

Darwin's diagram is not even connected at the base, as must be a genealogical tree. This presumably reflects his idea, as he put it in Notebook C in 1838: "The bottom of the tree of life is utterly rotten & obliterated in the course of [the] ages." His predecessors also had doubts about the base of the tree (notably Louis Agassiz and Edward Hitchcock), so that when they drew their diagrams of the fossil history of organisms they also were not connected to a single origin. Trémaux had no such doubts, and explicitly indicated a single origin and connected all of his lineages to it.

Ironically, Trémaux actually produced (quite independently) a finished version of an idea that Darwin sketched in one of his notebooks. This is on a page numbered 184 (probably from the early 1850s; see Charles Darwin's unpublished tree sketches). As shown below, it also considers the relationship between genealogical trees and geological history. Darwin owned a copy of Trémaux's book but apparently saw nothing of worth in it (Wilkins & Nelson 2008), in spite of the obvious relationship to his own idea!

Darwin's sketch

Circular trees apparently did not re-appear until the work of Engler (1881), where the concentric circles represented different morphological features, instead of geological time, thus showing phenotypic divergence from the common ancestor (along with the genealogy represented by the tree itself).

Conclusion

It is of some concern that Trémaux's book is so poorly known and the author himself almost unheard of. He does not appear in any of the standard histories of biology (see Wilkins & Nelson 2008), and his entry in the English-language Wikipedia has only two lines (he fares better in the French version)

In his 1874 book (Origine des Espèces et de l'Homme, avec les Causes de Fixité et de Transformation, et Principe Universel du Mouvement et de la Vie ou Loi des Transmissions de Force) Trémaux makes it clear that the [French] Académie des Sciences had rejected his work. Thereafter, few people seem to have read any of it, relying instead on the correspondence of Karl Marx (who thought the book was great) and Friedrich Engels (who though that it was rubbish) to pass judgement. Wilkins & Nelson (2008) have tried to redress the problem to some extent.

The rejection by the Académie is likely to have been because they did not accept the application of Darwinian evolution to humans. Indeed, it has been noted (see Hull 1988) that French biologists did not embrace Darwin's ideas in general. More particularly, Darwin himself realized that most of the problems engendered by his work would surround the idea of human evolution. Indeed, it was one major area where he and Alfred Russel Wallace (who independently developed the idea of natural selection) disagreed, as Wallace refused to apply the idea to humans.

Wilkins & Nelson (2008) wisely suggest that much of the confusion also comes from translating Trémaux's use of the French word "sol" as "soil" rather than as "habitat", thus leading to the conclusion that Trémaux was claiming that it is the nature of the soil alone that affects evolution. This was certainly done by Stephen Jay Gould (1997, 1999), who commented that: "I have never read a more absurd or more poorly documented thesis." Trémaux and his book deserve a better epitaph than that, because Trémaux certainly meant much more than most of the historical commentators have credited him with.

References

Engler A. (1881) Über die morphologischen Verhältnisse und die geographische Verbreitung der Gattung Rhus, wie der mit ihr verwandten, lebenden und ausgestorbenen Anacardiaceae. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 1: 365-426.

Gould S.J. (1997) Redrafting the Tree of Life. Proceedings of the American Philosophical Society 141: 30-54.

Gould S.J. (1999) A Darwinian gentleman at Marx's funeral. Natural History 108(7): 32-41. [Reprinted as "The Darwinian gentleman at Marx's funeral" in the book I Have Landed (2002).]

Hull D.L. (1988) Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science. University of Chicago Press, Chicago.

Wilkins J.S, Nelson G.J. (2008) Trémaux on species: A theory of allopatric speciation (and punctuated equilibrium) before Wagner. History and Philosophy of the Life Sciences 30: 179-206.

Steven Jay Gould was wrong

As always at the beginning of the week, this blog presents something in a lighter vein. However, this week we depart from the restricted world of phylogenetic networks and delve into the deeper waters of evolutionary processes.

In 1980 Steven Jay Gould published a chapter in a book about junk food (Phyletic size decrease in Hershey bars. Pages 178-179 in: C.J. Rubin, D. Rollert, J. Farago, R. Stark, J. Etra, eds. Junk Food. Dial Press/James Wade, New York), in which he tried to convince his readers that Cope's Rule of phyletic size increase applies to biological organisms but not to manufactured objects. He did this by analyzing the evolutionary history of Hershey bars, a chocolate confection well known to most Americans (but not to all that many others, at least in 1980).

I thought then, and I still think now, that Gould was wrong. I can think of several manufactured objects that show a size increase during their evolutionary history. Eventually, I decided that I could stand it no longer, and in 2000 I wrote about this in the Australian Systematic Botany Society Newsletter. I chose to write about the Evolutionary History of Mazda Motor Cars, because this manufactured object is not edible and is not well known to most Americans. I have linked to a PDF copy [1.6 MB] of the paper, because I figure that most of you have never heard of the ASBS Newsletter, and have therefore never read the article. You should.