I found a more systematic argument in a published scientific papers on this subject from the other side(i.e that evolution happened, but cannot be represented by a tree of life). The basic argument is that that the tree of life is a forced construct and not “real”. It touches most of teh important points and is a structured argument.
The paper is below -
http://www.pnas.org/content/104/7/2043
I will quote the paras which will give a gist of the argument (you can read the paper for a detailed understanding)
- Criteria for falsifying the tree of life -
Blockquote
The TOL hypothesis could be falsified by substantial failure of any of these propositions. First, and most fundamentally, the pattern of groups subordinate to groups might be illusory or artifactual, “the mere putting together and separating objects more or less alike” (16) in accordance to expectation. In this case there would be no explanandum, no all-embracing pattern or fact existing in nature and independent of our desire to impose order. Second, similarities between species used to erect the TOL (or any natural scheme) might not predominantly reflect common descent. Patterns of resemblance recognized by systematists could after all result from some natural cause other than direct (branching) descent with modification, such as environmental constraint and convergence, parallelism, or reticulation. Third, selection and branching species divergence might not be inevitably connected. Sometimes selection will drive reticulation [as with lateral gene transfer (LGT) of novel adaptations], whereas sometimes divergence will be produced by stochastic processes (drift).
- What will be argued for:
Blockquote
We will argue that inclusive hierarchical classifications do not emerge naturally and consistently from the relevant prokaryotic data considered in general (in their entirety). Instead, they have been imposed on them by selective analyses that are based on the assumption that a tree must be the real natural pattern, even if only certain of the data can be trusted to reveal it. Furthermore, we propose that the underlying historical processes affecting prokaryotes are more complex and various than those imagined by Darwin (or by neo-Darwinists), and not of necessity expected to give rise to a natural hierarchy.
- Being able to create trees is not the proof for Trees of Life -
Blockquote
The body of data (the explanandum) for which a hypothesis (the explanans) proposes to account cannot at the same time constitute proof for that hypothesis (17, 23), nor can further data of the same kind. We might construct a hierarchical taxonomy of Drosophila based on certain morphological characters and claim that its branching pattern reflects an evolutionary branching process. Adding more taxa would bush out the tree but not strengthen this fundamental claim about process, nor would adding more characters, necessarily, if there were reason to believe that by functional constraint these characters were correlated with the first set. Much of what has happened in post-Darwinian phylogenetics has been an enormous expansion of the explanandum (accepted from the outset by Darwin) by the addition of new taxa or characters (24–32). Moreover, this expansion has for the most part used algorithmic tools that are constrained to produce trees.
- Trees are assumed… and not proven -
Blockquote
In a search for independent evidence of a natural hierarchy, Panchen considers homology, paleontology, and biogeography. The first is problematic in that true (taxic) homologies cannot be distinguished from false ones (homoplasies) without some assumption of hierarchy: homologies are more often deduced from trees than trees are from homologies. Thus, explanans melds with explanandum, and neither is tested. The second and third may offer independent evidence that evolution by descent with modification has occurred but are limited in their relevance and applicability to specific groups, areas or times. They do not justify, except by extrapolation, the expectation that there should be groups under groups at all levels, that there should be a universal TOL, dichotomously branching all of the way down to a single root. Alternatives [extensive reticulation or separate origins from a common inchoate ancestral state (2, 14, 34)] can be entertained.
This is more or less what i am saying about convergence / homologs and homplasies.
4, Molecular Phylogenetics in Prokaryotes and implications -
Blockquote
Because there is substantial disagreement among prokaryotic molecular data sets and little strongly supported congruent signal among data sets that do not clearly disagree, a claim that a hierarchical pattern of groups subordinate to groups is the universal natural order cannot be sustained as an explanandum (6, 8, 18). (That many seemingly different analyses of these data nevertheless do agree in some ways is not surprising and is discussed later.)
- Tree of Life Vs Tree of cells -
Blockquote
Microbial phylogeneticists have not in general taken it to be their duty to confirm the existence of a natural inclusive hierarchy or tested the TOL hypothesis that this hierarchy is to be explained by an historical branching process. The ways in which they generally analyze and think about the molecular data presuppose a tree model, and cannot but produce trees. Even when methods that permit reticulated representations of evolution are used, the most common intent has been to discount LGT as noise, in pursuit of the legitimate “phylogenetic signal” assumed to be vertical unless significantly in conflict (11, 64, 40, 66). That is, weak signal is by default taken as vertical. Most importantly, the vast majority of analyses have consisted of the comparative evaluation of one tree with others (in search of the “true” branching topology). Seldom have investigators asked whether non-tree (reticulated) models might not better explain the data at hand. (Exceptions most often involve within-species data sets, where recombination is expected.)
Nevertheless, some phylogeneticists accept that LGT has been so pervasive over the history of life that no hierarchical classification can claim to provide the unique and true accounting of similarities and differences between organisms (and thus, an explanandum for Darwin’s explanans). Woese himself asks “What does it mean, then, to speak of an organismal genealogy when nearly all of the genes in the cell, genes that give it its general character, do not share a common history? This question goes beyond the classical Darwinian context”
The author of the paper readily accepts that we can create trees at the level of Animals. However, he denies that prokaryotes readily fall into a tree… and that modification happened in many cases by Lateral gene transfer. (Its interesting to note his field of interest is prokaryotes). This is equivalent to cutting off the trunk of the tree of life!
The final part of his argument is interesting-
Blockquote
Evolutionists have long acknowledged a diversity of population-level diversification mechanisms (selection, drift, convergence, and parallelism) and (with reservations) clade-level mechanisms that extend beyond the selectionist and gradualist framework mapped out by Darwin. At the genome level, vertical descent and LGT, gene creation, duplication and loss, in all combinations with population-level processes, expand the evolutionary repertoire. A multifaceted process pluralism is now the common view (79). The belief that nature must nevertheless exhibit a single pattern of true relationships among taxa remains vigorous, and fuels the continued enthusiasm for universal tree building and its broad application on the basis of very few and often contradictory data. We call this belief “pattern monism.” “Pattern pluralism” (the recognition that different evolutionary models and representations of relationships will be appropriate and true for different taxa or for different purposes) is an appealing alternative, and can defuse the crisis within the discipline.
Another interesting paper with respect to evolutionary trees and molecular genetics is below -
Perhaps a tree exists only is in the eyes of the beholder… (after cutting of all the “noise”)…