Wednesday, February 13, 2013

Pasta have no phylogeny (so don't try to give them one)


If you feed arbitrary data into a phylogenetic analysis then you will always get something out again, but it will in all probability be meaningless. For example, non-living objects do not have a phylogenetic history, at least not in the same way as living objects. Cultural objects certainly do have a history, and many aspects of that history may be similar to evolutionary patterns (see False analogies between anthropology and biology), but we cannot take it for granted that all historical patterns can be treated as analogous to those induced by evolution.

Even data that can be placed in a hierarchy do not necessarily represent a phylogeny — a phylogeny may well be a tree but not every tree is necessarily a phylogeny. Even having an evolutionary history does not mean that there is a phylogenetic history — for example, if the evolution is transformational then the history will be a chain rather than a tree or network.

Olivier Rieppel (2010) mentioned pasta as an example of this important distinction, because the features of pasta contain almost no phylogenetic information at all. Pasta has a history, sure, but it is not a phylogenetic history, in the Darwinian sense of variational evolution. Nor, incidentally, does pasta have a transformational history, either. The different types of pasta were not derived by a historical process of descent with modification, but are instead simply different expressions of a small set of basic ideas about what shapes you can make out of noodles (which are themselves little more than durum wheat flour mixed with water). The key feature of phylogenetic datasets is congruence among different character sets, and this is what we detect as phylogenetic signal, but there is no such congruence among the characteristics of pasta. (For a detailed analysis, with figures, see the interesting book by George Legendre 2011.)

In spite of this, pasta actually is used by many institutions (particularly in the USA) as an example to teach school and/or undergraduate students about phylogenetic analysis. I won't list them all here, but the simple Internet search that I just did quickly produced at least six of them. Here is an example datasheet from one of them, to illustrate the idea:


There are, unfortunately, many other examples of inanimate objects being used as introductory examples for phylogenetic analysis, even when those objects have no obvious phylogenetic history, including: Paper-clips (discussed by Petroski 1992); Nuts & bolts (discussed by Nickels & Nelson 2005); and Biscuits (discussed by Madden 2011).

This violates all common sense in phylogenetics. Indeed, it is actually anti-phylogenetics because it promolgates the idea that there is nothing special about evolutionary history, as distinct from any other sort of history. As noted by Erin Naegle (2009):
Biological organisms have descended from common ancestors. This is not true of manmade objects such as hardware or pasta. While constructing trees of objects may be motivating for students, such exercises are removed from evolutionary theory. Using inanimate objects may give students the impression that all trees are equally correct, since there is no inherently correct way to place objects on a tree.
Part of problem with almost all of these class exercises seems to be confusion between classification and phylogeny, since these seem frequently to be taught as part of the same exercise. As noted by Nickels & Nelson (2005):
Perhaps the most common — but ultimately self-defeating — approach in teaching about biological classification uses the arrangement of manufactured objects (hardware, furniture, whatever) in an attempt to illustrate the principles of biological classification. This approach assumes that classifying manufactured objects is fundamentally similar to classifying biological organisms. Unfortunately, this assumption is wrong in important ways  ...  simply put, taxonomic classifications of organisms are fundamentally different from the classifications of other things. And this distinction is the key point that students need to grasp.
All objects can be classified, and many objects can be classified using a hierarchical scheme, which can then be represented as a tree; but this does not make that tree a phylogeny. Classifications can be derived from any set of data, but they are particularly suitable for datasets with an intrinsic hierarchical pattern. Since the phylogenetic patterns in many groups of organisms are tree-like, they can be conveniently represented in a hierarchical classification. However, this logic cannot be inverted — just because we have a hierarchical classification does not mean that it came from a phylogenetic pattern.

I have always been acutely aware of this potential problem when I have used phylogenetic networks to analyze datasets where there is unlikely to be an evolutionary cause to the multivariate patterns, such as the Eurovision Song Contest, the FIFA World Cup, Scotch whiskies, Bordeaux wine, fast food, or lists of celebrities (see the Analyses page of this blog). In these cases I have explicitly emphasized that the analysis is intended as an Exploratory Data Analysis (EDA) not a phylogenetic analysis. This distinction is an important one in phylogenetics — any patterns detected by the EDA may, indeed, result from a phylogenetic history, but equally they may not do so. In this sense it is unfortunate that the output is still called a phylogenetic network.

I am not the first person to point out the problem of using inanimate objects for phylogenetics (Nickels & Nelson 2005; Naegle 2009; Meisel 2010). If anything, manufactured goods may provide a suitable example of horizontal transfer (Meisel 2010), but this seems a bit advanced for an introductory class of students.

Are there, then, any good examples that could be used to provide students with a simple and easy introduction to phylogenetic analysis? All that is required is that the objects actually have a phylogenetic history, and that a dataset for the objects can be collected by the students in a straightforward but entertaining manner.

As one example, Nelson & Nickels (2000) suggest using humans as the examplar, and there is a web page pursuing this idea at the Evolution and the Nature of Science Institutes. Alternatively, one could use the example of the fictional Caminalcules (Gendron 2000), which is discussed both here and here. Other examples are limited solely by your own imagination.

References

Gendron RP (2000) The classification & evolution of Caminalcules. American Biology Teacher 62: 570-576.

Legendre GL (2011) Pasta by Design. Thames & Hudson, London.

Madden D (2011) DNA to Darwin: Introductory Activities, Teacher's Guide. NCBE, University of Reading.

Meisel RP (2010) Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach 3: 621-628.

Naegle E (2009) Patterns of Thinking about Phylogenetic Trees: A Study of Student Learning and the Potential of Tree Thinking to Improve Comprehension of Biological Concepts. Doctor of Arts thesis, Idaho State University.

Nelson CE, Nickels MK (2000) Using humans as a central example in teaching undergraduate biology labs. In: Karcher SJ (editor) Tested Studies for Laboratory Teaching, Volume 22. Proceedings of the 22nd Workshop / Conference of the Association for Biology Laboratory Education (ABLE), pp 332-365.

Nickels MK, Nelson CE (2005) Beware of nuts and bolts: putting evolution into the teaching of biological classification. American Biology Teacher 67: 283-289.

Petroski H (1992) The evolution of artifacts. American Scientist 80: 416-420.

Rieppel O (2010) The series, the network, and the tree: changing metaphors of order in nature. Biology and Philosophy 25: 475-496.

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