Science Literature

The world of human phylogeny has been hit by a bombshell. Although scholars and textbooks are presenting chimpanzees as man's closest relatives, Grehan and Schwartz have revived the case for orangutans. They consider hominoids to be comprised of two sister clades: the human-orangutan clade (dental hominoids) and the chimpanzee-gorilla clade (African apes). They claim that humans and orangutans "share a common ancestor that excludes the extant African apes". Since it is received wisdom that chimps are the nearest relative to humans because we share over 98% of their genes and since humans are referred to as the "third chimpanzee", the ramifications of the new paper are immense!

Mr. Jiggs, a six-year-old orangutan at London Zoo, is capable of mopping his own quarters (credit B. A. Stewart and D. S. Boyer, source here)

Conceptual upheavals of this magnitude are unlikely to happen without major methodological modifications. This is the main concern of this blog. The authors do not start with DNA similarities but with morphological data. They note that, originally, the DNA comparisons were interpreted in the light of morphological analyses, but:

"Neither of two oft-cited morphological studies claiming to corroborate the interpretation of molecular data as supporting a close relationship between chimpanzees and humans took into consideration or provided justification for excluding most of the morphological features that have been documented as being shared uniquely by humans and orangutans."

The authors proceed to critique previous studies for the way they selected characters for cladistic analysis. They point out that these approaches incorporated characters considered to be derived within the ingroup "in spite of the fact that the feature is also common in the outgroup".

"Although a range of morphological studies have claimed to support a closer relationship between humans and chimpanzees or African apes, these studies have relied on many of the characters that we found to be problematic, and thus demonstrate how entrenched error becomes as it is unquestioningly passed on from and incorporated into one study after another."

Those familiar with the Kuhnian analysis of the practice of science will discern features here of 'working within the paradigm', with presuppositions unintentionally closing off avenues of enquiry. Conscious of the limitations of other work, Grehan and Schwartz explain and justify their selection of characters. One of their additional objectives was to include numerous fossil apes within their study.

"Our analysis of relationships between living and fossil taxa is based on a character matrix limited to hard-tissue characters that have been sufficiently well described in the literature to permit verification, and whose claimed character states as well as unique occurrence within a large-bodied hominoid clade we could corroborate via a broad outgroup comparison."

It is worth noting that their conclusion has deep roots. Schwartz was making points like this in 1984. His book The Red Ape appeared in 1987 and in a revised form in 2005. The paper has not come from authors who have suddenly hit on a quirky idea but it represents the mature judgment of two respected scholars.

What then shall be said of the DNA similarity data? The analysis of the authors is scathing. The key points are, in their own words:

"But the widely accepted notion that the 'greatest overall molecular similarity' is synonymous with 'most closely related' derives not from any empirical evidence but merely from the acceptance without question of the 'molecular assumption': namely, most recently divergent taxa will be most similar in their proteins and DNA because they will have shared a longer lineage of molecular change prior to their divergence and that the pace of molecular change was clocklike in nature. Nevertheless, despite claims to the contrary, the demonstration of molecular similarity does not a priori equate with a demonstration of homology, which must precede any hypothesis of phylogenetic relationship because a demonstration of similarity alone is only phenetic and must be subject to rigorous phylogenetic enquiry."

They cite previous work by Schwartz & Maresca that was the subject of a blog here. They argue that the published studies lack objectivity and have embedded tautologies. The New Scientist report summarises the argument against chimp/human genetic similarities by quoting one of the authors:

"Grehan, however, argues that this is not scientifically justified. He points out that traditional taxonomy makes a distinction between two types of similarity - "derived novelties" and "primitive retentions". Derived novelties are traits shared by two closely related species and are taken to have evolved in a recent common ancestor. Primitive retentions are older traits with a deeper evolutionary past shared by a larger group of species.
The problem with molecular systematics, says Grehan, is it fails to distinguish between the two. "It does not matter that more DNA similarities may be found between humans and chimpanzees if these similarities are really primitive retentions," he says."

A third element of the new paper is to set the argument for the human/orangutan relationship in a biogeographical context. Whereas the consensus view understands an emergence of humanity "out of Africa", there is a need for these issues to be addressed for the dental hominoid clade. The authors do this utilising data relating to the fossil species included in their analysis.

The significance of the paper is that the arguments relate to cladism (which is very widely used for assigning probabilities to evolutionary relationships) and phylogenomics (which is a standard tool for establishing evolutionary relationships). The authors have challenged the scientific consensus with some cogent and penetrating arguments. It is not just a dispute about the meaning of data, but how that data is selected and what presuppositions the researchers bring to their work. As such, the new paper provides us with a very important case study and sets the agenda for potentially very interesting discussions about methodology. If this is properly done, it will be to the health of the science community. Scientists with an openness to ID will welcome this debate, because many of critiques made by Grehan and Schwartz link directly to issues that concern us.

Evolution of the second orangutan: phylogeny and biogeography of hominid origins
Grehan, J.R. and Schwartz, J. H.
Journal of Biogeography, advance online 22 June 2009 | doi 10.1111/j.1365-2699.2009.02141.x (abstract)

Main conclusions: Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human-orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. [. . .]

See also:

Lawton, G. Could the orang-utan be our closest relative? New Scientist, 17 June 2009

Humans and Orangutan, Buffalo Museum of Science web resource.