Wednesday, January 2, 2013
False analogies between anthropology and biology
There has been much talk over the past few decades about the extent to which the various disciplines within anthropology (in the broad sense) can use, or benefit from, methodological techniques developed in other disciplines, notably biology (see Mace et al. 2005; Forster & Renfrew 2006; Lipo et al. 2006). This has been particularly true for historical studies of languages (ie. linguistics), past cultures (ie. archaeology) and physical type (ie. physical / biological anthropology). The use of, for example, phylogenetic methods seems to be relatively unproblematic in the latter case (studies of the origin and development of humans as a species; Holliday 2003), although this field is concerned as much with population genetics as it is with species phylogenies. (Note that I am leaving cultural anthropology out of the discussion, as it seems to be less concerned with historical studies.)
However, the use of phylogenetic methods in archaeology and linguistics is based on an analogy between human cultural evolution and biological evolution. This analogy assumes that the underlying processes of historical change in anthropology and biology are similar enough that the analytical methods can be combined. (Note that I am using the word anthropology in the broadest sense, to include linguistics and archaeology.) So, both anthropology and biology apparently involve an evolutionary process, in which the study objects form groups that change via modification of their intrinsic attributes, the attributes being transformed through time from ancestral to derived states (often called "innovations" in anthropology). That is, it is the groups of objects that change through time (variational evolution) rather than the objects themselves changing (transformational evolution). Thus, if one group acquires a new (derived or advanced) character state while the rest do not (i.e. they retain the ancestral or primitive state) then this group forms a separate historical lineage that diverges from the other populations, and maintains its own historical tendencies and fate. A search for derived character states that are shared among the groups allows us to reconstruct the evolutionary history.
However, this apparent similarity is basically a metaphor, because human culture is not a collection of biological objects. In Popperian terms, biology is part of the "world that consists of physical bodies" while culture and linguistics are part of the "world of the products of the human mind". Therefore, if we are drawing an analogy between anthropological studies and biological studies, and using this analogy to justify the use of certain analytical techniques, then we need to understand the analogy thoroughly. Here, I argue that in some important ways the currently used analogy is wrong from the biological perspective, and that this has important consequences for anthropological research.
The analogy between anthropology and biology has recently focused on the possible relationship between anthropological entities and genes (eg. Mace & Holden 2005; Tëmkin & Eldredge 2007; Croft 2008; Pagel 2009; Steele et al. 2010; Howe & Windram 2011). However, this seems to be a false analogy, as there is no observable equivalent to a gene in the anthropological world (other than inside any biological organisms being studied). Memes, for example, are not observable objects in the way that genes are. So, the analogy between real replicators in biology (genes) and theoretical replicators in anthropology is inappropriate.
However, biology recognizes a distinction between genotype, which is the collection of genes and other associated material in an organism, and phenotype, which is the product of interactions between genes and also between genes and their environment. The DNA, RNA and proteins in an organism are usually taken to represent the genotype, whereas the cells, tissues and organs constitute the phenotype of an individual. To quote Richard Lewontin (in the Stanford Encyclopedia of Philosophy): "the actual correspondence between genotype and phenotype is a many–many relation in which any given genotype corresponds to many different phenotypes and there are different genotypes corresponding to a given phenotype."
The better analogy between anthropology and biology is thus with the phenotype, not the genotype. Genetic material stores information that allows it to replicate itself, either exactly or with modification, and this is the basis of the distinction between living and non-living objects. Nothing in archaeology or linguistics, for example, possesses these properties, and to form an analogy between anthropological entities and genes is thus potentially misleading. In particular, genetic material is based on standardized fundamental units (the nucleotides and amino acids), which have no simple counterpart in anthropology.
An analogy between anthropological entities and phenotypes is much more reasonable, however. Phenotypic entities, such as cells and organs, seem to have much more in common conceptually with anthropological entities, such as phonemes and words in linguistics and stemmatology. Most importantly, it is the phenotype that takes part in evolutionary processes, not the genotype alone (genes are just part of the "replicator story", as DNA on its own does nothing except denature slowly), and so it is actually the more useful comparison. Indeed, up until the 1990s phenotypes were the basic unit of phylogenetics in biology, and it is only since then that biologists have switched wholesale to genotypes for constructing phylogenies. Anthropologists cannot make this switch, and need to remain "phenotype phylogeneticists" instead.
The important point to note is that evolutionary anthropology is a study of historical relationships rather than specifically "genetic" ones. That is, while cultural transmission is qualitatively different from genetic transmission, that does not invalidate a study of history. Genes are passed directly to offspring whereas culture involves behaviour that is transmitted by social learning; for example, manuscripts are copied by hand, languages are learned by imitating parents, and musical instruments are deliberately designed by professionals. Biological transmission is thus different from anthropological transmission, but both types of transmission produce a history.
Phenotypes have historical relationships just as genotypes do, as is now recognized by the resurgence of interest in evolutionary developmental biology (also known as evo-devo). No analogy with genetics is necessary for evolutionary studies of anthropology. Moreover, not all genetic relationships are necessarily evolutionary (much of population genetics, for example, can be conducted without an evolutionary framework), although it is likely that they will all have a strong evolutionary component. (Note that in anthropology vertical phylogenetic descent is sometimes confusingly referred to as the "genetic relationship", perhaps as a result of Noam Chomsky's work, and phylogenies are sometimes referred to as "classifications".)
Since phenotypes evolve, they can be an appropriate unit of study in phylogenetics, and can therefore can be an appropriate analogue for the study of cultural histories. The distinction between genotype and phenotype as the appropriate analogy is not a trivial one. In particular, the change of perspective seems to make clearer a number of issues that have been raised concerning the application of phylogenetic methods in anthropology.
First, it is often difficult to work out the homologies between phenotypic entities from divergent groups, just as it is for anthropological entities. If phylogenetics is a search for shared derived characters states, then we need to be comparing the same character states in different groups (ie. comparing like with like based on common ancestry). However, shared derived character states are not conveniently labeled as such on the objects themselves. We thus need to infer homology before we can infer phylogeny (or at least do this simultaneously), and this is often more difficult for phenotypes than for genotypes.
Phenotypic homology sometimes causes confusion even among evolutionary biologists. The basic issue is often which features should been seen as different states of the same character. As a cultural example, Tëmkin & Eldredge (2007) discuss the problem of the valves in a cornet, as "the Périnet valve did not derive from the Stölzel valve but rather was an alternative design solution" (alternative designs are quite common for manufactured objects). Thus, neither can be considered to be the ancestral state of a single character (valve type), even though the Stölzel valve predated the Périnet. Most biologists would solve this "problem" by having two separate characters, so that each valve type is either present or absent, thus effectively having a combined total of four character states. This allows a cornet to have either all Stölzel or all Périnet valves, or a combination of both (which a few instruments do have; Eldredge 2002). A cornet that has neither type of valve is called a post horn, this being the instrument from which the cornet was originally derived.
The search for an objective method of determining phenotypic homology has been a long one (Rieppel 2007), and is not by any means resolved; perhaps the most interesting discussion of an objective procedure is that of Jardine (1967). In particular, homoplasy (convergence / parallelism / reversal) is often a phenotypic phenomenon, as the genotype of the organisms concerned is almost always different in some way. That is, phenotypic homoplasy is usually the result of mistaken homology assessment, whereas genotypic homoplasy usually results from the fact that there are so few units of comparison (eg. four nucleotides). It has been suggested that homoplasy may be even more common in anthropology than in biology (Tëmkin & Eldredge 2007). Indeed, in culture it can be difficult even to decide on the units of comparison (eg. phonemes? syllables? words?), which is quite characteristic of phenotypic studies, and the "taxa" often need to be constructed for analysis (eg. tools, customs, etc).
Furthermore, it is likely to be inappropriate to use an analogy with molecular sequence alignment when discussing cultural and linguistic homologies (Covington 1996; Kondrak 2003; Pagel 2009). Computerized algorithms are usually used to align molecular data and thus make decisions about character-state homology, mostly based on overall similarity. However, homology of phenotypic characteristics requires careful comparative studies to determine what are called topological relations (or connectivity) among the character states, often based on ontogenetic development (Rieppel 2007); this is called "special similarity". It might be difficult to use ontogeny as an analogue for cultural development, since ontogeny refers to the sequential expression of genes, but topological relationships have obvious analogues in linguistics; for example, words consist of both primary structure (phonemes) and secondary structure (morphemes) (List 2012).
Second, it is likely that there will be a greater degree of reticulate evolution in archaeological and linguistic studies. This conclusion follows from the differences in barriers to horizontal flow of information — there are both weak and strong barriers in biology but only weak ones in anthropology.
In biology there are both pre-zygotic and post-zygotic barriers to gene flow, which refer to those acting to prevent the formation of a zygote and those acting after zygote formation, respectively. It is the latter that are most effective in creating reproductive isolation between taxa. Pre-zygotic mechanisms, such as geographical isolation (different locations), ecological isolation (different habitats), temporal isolation (different times), mechanical isolation (different physical structures) and ethological isolation (different behaviours), have obvious analogues in anthropological studies, but these barriers are often not completely effective, such as when species that were previously spatially separated encounter each other for the first time. Post-zygotic mechanisms, such as cross-incompatibility (inability of gametes to fuse), hybrid inviability (failure of zygotes to survive), hybrid sterility (failure of zygotes to reproduce) and hybrid breakdown (failure of second generation hybrids to survive), are strictly genetic mechanisms and they have no obvious analogue in anthropological studies. They are usually very effective barriers to gene flow, and indeed are the principal basis of the biological species concept, for example.
The important point to note is that the post-zygotic barriers are directly under genetic control whereas the pre-zygotic barriers are only indirectly genetically controlled (eg. habitat selection might be genetically determined, and if their habitats are different then two species will be reproductively isolated). This means that the post-zygotic barriers are much stronger. It also means that they are not available in the analogy between anthropology and phenotype.
Weak barriers mean that archaeological and linguistic aggregations are likely to form fuzzy clusters rather than clearly defined groups, just as they do for human races (Fuzzy clusters). Fuzzy clusters are not likely to form clear-cut evolutionary lineages, at least as far as vertical descent is concerned (Eldredge 2011).
Thus, because anthropological studies involve only weak barriers to the horizontal flow of information, reticulate evolution is predicted to be more prevalent than it is in biology. That is, the horizontal component of evolution may even be as large as the vertical one (and possibly more important), because there are none of the strong genetic ("post-zygotic") barriers to flow. Indeed, the use of trees as a model for archaeological and linguistic studies has been questioned repeatedly in recent years, on various grounds (eg. Southworth 1964; Hoenigswald 1990; Moore 1994; Dewar 1995; Ben Hamed & Wang 2006; Tëmkin & Eldredge 2007), usually in favor of reticulation models. Moreover, the earliest representations of historical relationships were networks rather than trees (Gallet), even in biology (Buffon, Duchesne), and since then many alternative reticulation metaphors have been developed (Metaphors). This suggests that the focus on trees has been a distraction from the more obvious model of a network in anthropology.
Networks and trees
One point of confusion here seems to be that trees have been treated as representations of temporal relationships while networks have been treated as representations of spatial relationships. Indeed, this seems to be at the heart of the apparent differences of opinion about the two models — the tree advocates are emphasizing time whereas the network advocates are emphasizing space. The practical problem here is that there are currently no quantitative methods for combining the two. Tree-building algorithms in biology do not allow for reticulation, and the common network algorithms (such as neighbor-net, median-joining, reduced median) solely show static relationships, without any sense that the inferred nodes represent ancestors or the edges connecting the nodes represent evolutionary change. In these commonly used algorithms, the nodes are there solely to support the network structure, and the edges solely express the degree of character difference between the nodes.
For phylogenetic trees there is a rationale for treating the tree diagram as a representation of evolutionary history. For example, in a study of a set of gene sequences, first we produce a mathematical summary of the the data based on a quantitative model. We then infer that this summary represents the gene history, based on the Hennigian logic that the patterns are formed from a nested series of shared derived character states (this is a logical inference about the biology being represented by the mathematical summary). We then infer that this gene history represents the organismal history, based on the practical observation that gene changes usually track changes in the organisms in which they occur (ie. a pragmatic inference). However, no such rationale exits for most of the current network methods. The network still represents a mathematical summary of the data, but there is no logic for direct inference about biology. It is almost certain that the mathematical summary represents real biological patterns, but there is no necessity that those patterns are evolutionary ones.
The increasing appearance of neighbor-net networks in the linguistic and archaeological literature (eg. Ben Hamed 2005; Bryant et al. 2005; Bowern 2010; Gray et al. 2010; Heggarty et al. 2010; Dediu & Levinson 2012), for example, is thus based on trying to infer temporal patterns from the network display of spatial patterns, even though there is no explicit rationale for being able to do this — the networks may represent history and they may not. Clearly, what we need are quantitative methods that allow the direct inference of both vertical and horizontal evolutionary patterns — that is, we need phylogenetic networks rather than phylogenetic trees. Moreover, these networks need to be based on models of phenotypic variation not genotypic variation (eg. Lewis 2001). Nakhleh et al. (2005), Warnow et al. (2006) and Erdem et al. (2006) are among the few to have tackled this issue in anthropology.
Note that none of the above discussion is meant to contrast a tree model with a network model in a mutually exclusive way. Mathematically, trees form a subset of networks. Therefore, we do not need to choose between the two as the most appropriate model — we can always choose a network model, and the resulting network will be more or less tree-like depending on the data. So, it is not necessary to decide wether anthropological data are more or less tree-like than biological data (Collard et al. 2006), nor should it be necessary to decide whether horizontal transmission invalidates cultural phylogenetic trees (O'Brien et al. 2002; Greenhill et al. 2009; Currie et al. 2010b) — we should simply incorporate any reticulations into the phylogeny rather than decide they are too small to need to include them.
In this sense, many of the recent anthropological papers that are based solely on a tree model seem to be misguided, no matter how sophisticated the mathematics of their analyses may be (Gray & Atkinson 2003; Gray et al. 2009; Currie et al. 2010a; Dunn et al. 2011; Gray et al. 2011; Bouckaert et al. 2012). For example, if a dataset is admittedly affected by horizontal transfer, it is unlikely that any tree-building algorithm will correctly construct the tree-like pattern of vertical descent. Thus, even if our model for evolutionary history is "a tree obscured by vines", we will still find it difficult to reconstruct the tree unless we explicitly move the vines out of the way first. It is for this reason, for example, that in linguistics many studies are based on the Swadesh list of words, which is clearly (and intentionally) biased towards words that have been inherited vertically, with little or no horizontal transfer (eg. Bouckaert et al. note: "the cognate data we use excludes known cases of borrowing"). Under these circumstances, it is hardly surprising that authors so often find their phylogenies to be tree-like, since they are deliberately ignoring the vines! Networks are likely to reveal both the tree and the vines (eg. otherwise hidden lexical borrowing; Nelson-Sathi et al. 2011).
Finally, it is worth mentioning the network methods that have been developed for within-species (ie. population) data, particularly mtDNA sequences. These include those methods related to median networks (eg. median-joining, reduced median), but also include those related to one-step networks (eg. statistical parsimony, minimum-spanning). In many anthropological situations, it is likely that these will be more useful than methods related to phylogenetic trees (see the examples in Barbrook et al. 1998; Forster et al. 1998; Forster & Toth 2003; Spencer et al. 2004; Lipo 2006). Bouckaert et al. (2012) take this analogy even further, by using a phylogeny-based epidemiological model of population spread.
The third consequence of rejecting the genotype analogy is that time inconsistency is no longer required. Organisms store the information (that is vertically and horizontally transmitted) in genes that they carry with them, which restricts reticulation to occurring only between contemporaries. However, while cultural aretefacts clearly display their information, they do not transmit it themselves, and it must instead be interpreted by humans. Furthermore, language and culture store their "information" externally, either in the minds of people or in permanent or semi-permanent records (either written or pictorial).
Thus, in anthropology the information available for horizontal transmission can come from the distant past, as well as from the present — the only direction that cultural information cannot flow is from the future to the past. In this sense, extinction seems to be much rarer in archeology and linguistics than in biology, because information can be stored indefinitely, rather than disappearing along with the possessing species. I have illustrated time inconsistency twice before, with respect to both computers and computer languages, and Tëmkin & Eldredge (2007) illustrate it with musical instruments.
Part of the issue here is also that archaeological objects are often not contemporaneous, whereas most biological studies are based on data from contemporary organisms (Lipo 2006). This means that in archaeological phylogenetics the study objects appear at internal nodes in the phylogeny as well as at the tips (the data are diachronic), whereas in biology they occur only at the tips (the internal nodes are hypothetical ancestors). In this case, it may be better to consider an archaeological analogy with the incorporation into the phylogenetic histories of full stratigraphic information from fossils (eg. Sumrall 2005; Tëmkin & Eldredge 2007; Fisher 2008).
Historical anthropology is often concerned with "origins" and putting dates on those origins (Gray et al. 2011), and therefore the study interest is where the analytical uncertainty is greatest, since this is the place where there are fewest data. This is quite different to much of the use of phylogenetic techniques in biology, where the relationships of contemporary organisms are the primary interest. Of particular concern are estimates of rates of divergence, for which there appear to be few mathematical models in archaeology. Small changes in rates can have large effects on estimates of origins and their dates, as can changes of rates along lineages.
Disconnection of phenotype and phylogeny
The fourth consequence is that there is often a lack of association between phylogeny and phenotype. There are examples in the literature of phenotypic changes not being directly associated with the phylogeny. Losos (2011) discusses a number of these within biology, and Tëmkin & Eldredge (2007) discuss a couple of cultural examples. In these cases, it is not possible to reconstruct the evolutionary history from phenotypic data, nor indeed to infer the phenotypes from an hypothesis of evolutionary history. In these cases phylogenetics does not aid the study of contemporary patterns.
This is particularly relevant when attempting to reconstruct ancestral phenotypes. Because of the difference between cultural transmission (copied from person to person) and biological transmission (genes are passed directly), there is no necessary reason to assume that ancestral states can be reconstructed from a knowledge of phylogenetic history (see the Evolving Thoughts blog). This also applies when trying to reconstruct characteristics from an independent phylogeny, such as reconstructing a cultural history from a linguistic phylogeny (eg. Walker et al. 2012).
Furthermore, it is possible that archaeological and linguistic concepts (eg. cultural artefacts and languages, respectively) do not form integrated wholes, in the way that biological organisms must. That is, anthropological characters (or groups of characters) can often change independently of each other, and this will create a set of independent phylogenetic histories, so that there is no coherent "entity" with a single history. This situation is likely to be worse than the possibly analogous situation with independent gene histories in biology (Tëmkin & Eldredge 2007).
In addition, cultural evolution may occur faster than biological evolution (Perreault 2012), which makes reconstruction of ancient events more difficult. We might also question whether different cultural artefacts and languages each share a single common ancestor — that is, they are potentially polyphyletic rather than monophyletic.
Finally, we can consider possible analogies of anthropological processes with horizontal genotypic processes, such as introgression, hybridization, recombination, horizontal gene transfer (HGT), and genome fusion. These analogies are sometimes invoked in the linguistic and archaeological literature, but this is not necessarily appropriate given the overall analogy with phenotype rather than genotype.
Introgression is usually treated as a process of admixture, where genetic information from one group moves to another via sexual reproduction. Here, an analogy might be appropriate for anthropology, it being the closest analogy to what anthropologists have called "diffusion". However, it is worth noting that biological admixture initially involves the move of an entire copy of the genome, which might be unlikely for cultural phenomena. Hybridization, on the other hand, involves the creation of a new evolutionary lineage, separate from the parental ones but containing one or more copies of the genome of each of those parents. Creole languages might be an example where this analogy is appropriate, since the parental languages are usually clearly identifiable; but otherwise hybridization seems to be a poor analogy, even though it is commonly invoked in the literature.
Recombination also involves sexual reproduction, but usually refers to the mixing of genes before reproduction occurs, so that the offspring do not have a complete set of genes from any one grandparent. This analogy frequently appears in the literature, often as a synonym for the same phenomena that other people call hybridization, but I suspect that introgression would be a better analogy for the topics included. Examples analogous to recombination might be a single manufacturer "providing all permutations and combinations to the marketplace" of their products (eg. Courtois' cornets in the late 1850s; Eldredge 2002), or where "a scribe used more than one copy of a text when making his or her own" (called contamination; Howe & Windram 2011).
HGT refers to non-sexual transfer of genetic material, often small amounts rather than whole genomes. Clearly, word borrowing would be a prime example where this analogy might be appropriate. Genome fusion refers to the non-sexual transfer of whole genomes, and thus has a similar outcome to hybridization, but between distantly related organisms instead.
We need to drop the idea that there is an analogy between anthropological entities and biological genotypes, and recognize that the better analogy is with phenotypes. The analogy with genotypes is not a productive one, and may even be a positively misleading form of "gene envy". If we accept the qualitative analogy with phenotype, then we can also accept the quantitative consequences of this analogy, which include the idea that trees are much more likely to be inadequate models for cultural history than they apparently are in biology.
The mere fact that one can interpret certain cultural phenomena as showing features analogous to those in biology does not mean that the alleged analogy is of any practical use. We need to understand the analogies more thoroughly, in order to decide whether adopting the analogies is the best thing to do. Analogies are only useful tools for research if they direct that research into productive areas, or provide interpretive insights that would otherwise be unavailable. Otherwise, analogy is merely a topic of conversation.
The main advantage of the phylogenetic analogy is that it focuses attention on the important role of unique "accidents" in determining evolutionary history. The main disadvantage seems to be that the processes involved with these accidents are quite different in biology and anthropology, so that the focus is not always fruitful.
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