"The Great Chain of Being" and the infinite chain of objectification

There has been a constant stream of evidence contradicting humanity's most cherished beliefs, including the "presence" of a supreme being in the natural order of things we call "evolution". Yet, despite the apparent snake-like sequence of evolution, the Western civilization's pyramid design (used to justify its ranking of humans on top of this chain) loses sight of scientific rigour to merely justify an opportunistic master versus the meek servants and other exploitative resources narrative...

Whilst even chimpanzees seem to have learnt how to outwit human hunters (http://news.bbc.co.uk/earth/hi/earth_news/newsid_8962000/8962747.stm), there is a lot more than meets the eye in this rather complex matter. For those wishing to voice a more informed opinion, it may be useful to consult the material published below, in the ScienceWeek Journal (http://scienceweek.com/2005/sw050624-3.htm).

ScienceWeek

EVOLUTION: ON THE GREAT CHAIN OF BEING

The following points are made by Sean Nee (Nature 2005 435:429):

1) For centuries the "great chain of being" held a central place in Western thought. This view saw the Universe as ordered in a linear sequence starting from the inanimate world of rocks. Plants came next, then animals, men, angels and, finally, God. It was very detailed with, for example, a ranking of human races; humans themselves ranked above apes above reptiles above amphibians above fish. This view even predicted a world of invisible life in between the inanimate and the visible, living world, long before Antonie van Leeuwenhoek's discoveries. Although advocates of evolution may have stripped it of its supernatural summit, this view is with us still.

2) Common presentations of evolution mirror the great chain by viewing the process as progressive. For example, in their book THE MAJOR TRANSITIONS IN EVOLUTION, John Maynard Smith and Eors Szathmáry take us from the origin of life, through to the origin of eukaryotic cells, multicellularity, human societies and, finally, of language. They explicitly point out that evolution does not necessarily lead to progress, and even refer to the great chain by its Latin name, scala naturae. But it is impossible to overlook the fact that the "major" evolutionary transitions lead inexorably, step by step, to us. Similarly, in their recent essay in Nature, "Climbing the co-evolution ladder" (Nature 431, 913:2004), Lenton and colleagues illustrate their summary of life-environment interactions through the ages with a ladder whose rungs progress through microbes, plants, and, at the top, large animals.

3) In his recent book THE ANCESTOR'S TALE, Richard Dawkins reverses the usual temporal perspective and looks progressively further back in time to find our ancestors. Like Maynard Smith and Szathmáry, he cautions us against thinking that evolution is progressive, culminating with us. He emphasizes that with whatever organism we begin the pilgrimage back through time, we all are reunited at the origin of life. But by beginning the journey with us and looking backwards along our ancestry, Dawkins generates a sequence of chapter titles that would read like a typical chain to a medieval theologian, albeit with some novelties and the startling omission of God.

4) By starting with us, Dawkins regenerates the chain because species that are more closely related to us are more similar as well, and such similarity was an important criterion in determining the rankings in the classical chain. But there is nothing about the world that compels us to think about it in this way, suggesting, instead, that we have some deep psychological need to see ourselves as the culmination of creation. Illustrating this, when we represent the relationships between species, including ourselves, in a family tree, we automatically construct it so that the column of species' names forms a chain with us as the top, as in the first of the trees pictured. But the other construction is equally valid.

References:

1. Lovejoy, A. O. The Great Chain of Being (Harper and Row, New York, 1965)

2. Gee, H. Nature 420, 611 (2002)

3. Maynard Smith, J. and Szathmáry, E. The Major Transitions of Evolution (W. H. Freeman & Co., Oxford, 1995)

4. Dawkins, R. The Ancestor's Tale (Weidenfeld & Nicolson, New York, 2004)

5. Nee, S. Nature 429, 804-805 (2004).


Nature http://www.nature.com/nature


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Related Material:

EVOLUTIONARY BIOLOGY: ON THE SCHEME OF ANIMAL PHYLA

The following points are made by M. Jones and M. Blaxter (Nature 2005 434:1076):

1) Despite the comforting certainty of textbooks and 150 years of argument, the true relationships of the major groups (phyla) of animals remain contentious. In the late 1990s, a series of controversial papers used molecular evidence to propose a radical rearrangement of animal phyla [1-3]. Subsequently, analyses of whole-genome sequences from a few species showed strong, apparently conclusive, support for an older view[4-6]. New work [7] now provides evidence from expanded data sets that supports the newer evolutionary tree, and also shows why whole-genome data sets can lead phylogeneticists seriously astray.

2) Traditional trees group together phyla of bilaterally symmetrical animals that possess a body cavity lined with mesodermal tissue, the "coelom" (for example, the human pleural cavity), as Coelomata. Those without a true coelom are classified as Acoelomata (no coelom) and Pseudocoelomata (a body cavity not lined by mesoderm). We call this tree the A-P-C hypothesis. Under A-P-C, humans are more closely related to the fruitfly Drosophila melanogaster than either is to the nematode roundworm Caenorhabditis elegans[5,6].

3) In contrast, the new trees [1-3,7] suggest that the basic division in animals is between the Protostomia and Deuterostomia (a distinction based on the origin of the mouth during embryo formation). Humans are deuterostomes, but because flies and nematodes are both protostomes they are more closely related to each other than either is to humans. The Protostomia can be divided into two "superphyla": Ecdysozoa (animals that undergo ecdysis or moulting, including flies and nematodes) and Lophotrochozoa (animals with a feeding structure called the lophophore, including snails and earthworms). We call this tree the L-E-D hypothesis. In this new tree, the coelom must have arisen more than once, or have been lost from some phyla.

4) Molecular analyses have been divided in their support for these competing hypotheses. Trees built using single genes from many species tend to support L-E-D, but analyses using many genes from a few complete genomes support A-P-C [5,6]. The number of species represented in a phylogenetic study can have two effects on tree reconstruction. First, without genomes to represent most animal phyla, genome-based trees provide no information on the placement of the missing taxonomic groups. Current genome studies do not include any members of the Lophotrochozoa. More notably, if a species' genome is evolving rapidly, tree reconstruction programs can be misled by a phenomenon known as long-branch attraction.

5) In long-branch attraction, independent but convergent changes (homoplasies) on long branches are misconstrued as "shared derived" changes, causing artefactual clustering of species with long branches. Because these artefacts are systematic, confidence in them grows as more data are included, and thus genome-scale analyses are especially sensitive to long-branch attraction. Long branches can arise in two ways. One is when a distantly related organism is used as an "outgroup" to root the tree of the organisms of interest. The other is when one organism of interest has a very different, accelerated pattern of evolution compared with the rest.


References (abridged):

1. Aguinaldo, A. M. A. et al. Nature 387, 489-493 (1997)

2. Winnepenninckx, B. et al. Mol. Biol. Evol. 12, 1132-1137 (1995)

3. Adoutte, A., Balavoine, G., Lartillot, N. & de Rosa, R. Trends Genet. 15, 104-108 (1999)

4. Mushegian, A. R., Garey, J. R., Martin, J. & Liu, L. X. Genome Res. 8, 590-598 (1998)

5. Blair, J. E., Ikeo, K., Gojobori, T. & Hedges, S. B. BMC Evol. Biol. 2, 7 (2002)

6. Wolf, Y. I., Rogozin, I. B. & Koonin, E. V. Genome Res. 14, 29-36 (2004)

7. Philippe, H., Lartillot, N. & Brinkmann, H. Mol. Biol. Evol. 22, 1246-1253 (2005)


Nature http://www.nature.com/nature

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Related Material:

EVOLUTION: GENOMES AND THE TREE OF LIFE

The following points are made by K.A. Crandall and J.E. Buhay (Science 2004 306:1144):

1) Although we have not yet counted the total number of species on our planet, biologists in the field of systematics are assembling the "Tree of Life" (1,2). The Tree of Life aims to define the phylogenetic relationships of all organisms on Earth. Driskell et al (3) recently proposed a computational method for assembling this phylogenetic tree. These investigators probed the phylogenetic potential of ~300,000 protein sequences sampled from the GenBank and Swiss-Prot genetic databases. From these data, they generated "supermatrices" and then super-trees.

2) Supermatrices are extremely large data sets of amino acid or nucleotide sequences (columns in the matrix) for many different taxa (rows in the matrix). Driskell et al (3) constructed a supermatrix of 185,000 protein sequences for more than 16,000 green plant taxa and one of 120,000 sequences for nearly 7500 metazoan taxa. This compares with a typical systematics study of, on a good day, four to six partial gene sequences for 100 or so taxa. Thus, the potential data enrichment that comes with carefully mining genetic databases is large. However, this enrichment comes at a cost. Traditional phylogenetic studies sequence the same gene regions for all the taxa of interest while minimizing the overall amount of missing data. With the database supermatrix method, the data overlap is sparse, resulting in many empty cells in the supermatrix, but the total data set is massive.

3) To solve the problem of sparseness, the authors built a "super-tree" (4). The supertree approach estimates phylogenies for subsets of data with good overlap, then combines these subtree estimates into a supertree. Driskell et al (3) took individual gene clusters and assembled them into subtrees, and then looked for sufficient taxonomic overlap to allow construction of a supertree. For example, using 254 genes (2777 sequences and 96,584 sites), the authors reduced the green plant supermatrix to 69 taxa from 16,000 taxa, with an average of 40 genes per taxon and 84% missing sequences! This represents one of the largest data sets for phylogeny estimation in terms of total nucleotide information; but it is the sparsest in terms of the percentage of overlapping data.

4) Yet even with such sparseness, the authors are still able to estimate robust phylogenetic relationships that are congruent with those reported using more traditional methods. Computer simulation studies (5) recently showed that, contrary to the prevailing view, phylogenetic accuracy depends more on having sufficient characters (such as amino acids) than on whether data are missing. Clearly, building a super-tree allows for an abundance of characters even though there are many missing entries in the resulting matrix.


References (abridged):


1. M. Pagel, Nature 401, 877 (1999)

2. A new NSF program funds computational approaches for "assembling the Tree of Life" (AToL). Total AToL program funding is $13 million for fiscal year 2004. NSF, Assembling the Tree of Life: Program Solicitation NSF 04-526 (www.nsf.gov/pubs/2004/nsf04526/nsf04526.pdf)

3. A. C. Driskell et al., Science 306, 1172 (2004)

4. M. J. Sanderson et al., Trends Ecol. Evol. 13, 105 (1998)

5. J. Wiens, Syst. Biol. 52, 528 (2003)


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