In the 1990s, research into the genetic codes of living things worsened the quandary faced by the theory of evolution in this regard. In these experiments, instead of the earlier comparisons that were limited to protein sequences, "ribosomal RNA" (rRNA) sequences were compared. From these findings, evolutionist scientists sought to establish an "evolutionary tree." However, they were disappointed by the results.

According to a 1999 article by French biologists Hervé Philippe and Patrick Forterre, "with more and more sequences available, it turned out that most protein phylogenies contradict each other as well as the rRNA tree."301

Besides rRNA comparisons, the DNA codes in the genes of living things were also compared, but the results have been the opposite of the "tree of life" presupposed by evolution. Molecular biologists James A. Lake, Ravi Jain and Maria C. Rivera elaborated on this in an article in 1999:

…[S]cientists started analyzing a variety of genes from different organisms and found that their relationship to each other contradicted the evolutionary tree of life derived from rRNA analysis alone.302

Neither the comparisons that have been made of proteins, nor those of rRNAs or of genes, confirm the premises of the theory of evolution. Carl Woese, a highly reputed biologist from the University of Illinois, admits that the concept of "phylogeny" has lost its meaning in the face of molecular findings in this way:

No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various [groups] to the makeup of the primary groupings themselves.303

The fact that results of molecular comparisons are not in favor of, but rather opposed to, the theory of evolution is also admitted in an article called "Is it Time to Uproot the Tree of Life?" published in Science in 1999. This article by Elizabeth Pennisi states that the genetic analyses and comparisons carried out by Darwinist biologists in order to shed light on the "tree of life" actually yielded directly opposite results, and goes on to say that "new data are muddying the evolutionary picture":

A year ago, biologists looking over newly sequenced genomes from more than a dozen microorganisms thought these data might support the accepted plot lines of life's early history. But what they saw confounded them. Comparisons of the genomes then available not only didn't clarify the picture of how life's major groupings evolved, they confused it. And now, with an additional eight microbial sequences in hand, the situation has gotten even more confusing.... Many evolutionary biologists had thought they could roughly see the beginnings of life's three kingdoms... When full DNA sequences opened the way to comparing other kinds of genes, researchers expected that they would simply add detail to this tree. But "nothing could be further from the truth," says Claire Fraser, head of The Institute for Genomic Research (TIGR) in Rockville, Maryland. Instead, the comparisons have yielded many versions of the tree of life that differ from the rRNA tree and conflict with each other as well...304

Comparisons that have been made of proteins, rRNA and genes reveal that creatures which are allegedly close relatives according to the theory of evolution are actually totally distinct from each other. Various studies grouped rabbits with primates instead of rodents, and cows with whales instead of horses.

In short, as molecular biology advances, the homology concept loses more ground. Comparisons that have been made of proteins, rRNAs and genes reveal that creatures which are allegedly close relatives according to the theory of evolution are actually totally distinct from each other. A 1996 study using 88 protein sequences grouped rabbits with primates instead of rodents; a 1998 analysis of 13 genes in 19 animal species placed sea urchins among the chordates; and another 1998 study based on 12 proteins put cows closer to whales than to horses.

As life is investigated on a molecular basis, the homology hypotheses of the evolutionary theory collapse one by one. Molecular biologist Jonathan Wells sums up the situation in 2000 in this way:

Inconsistencies among trees based on different molecules, and the bizarre trees that result from some molecular analyses, have now plunged molecular phylogeny into a crisis.305

But in that case what kind of scientific explanation can be given for similar structures in living things? The answer to that question was given before Darwin's theory of evolution came to dominate the world of science. Men of science such as Carl Linnaeus and Richard Owen, who first raised the question of similar organs in living creatures, saw these organs as examples of "common design." In other words, similar organs or similar genes resemble each other not because they have evolved by chance from a common ancestor, but because they have been designed deliberately to perform a particular function.

Modern scientific discoveries show that the claim that similarities in living things are due to descent from a "common ancestor" is not valid, and that the only rational explanation for such similarities is "common design."

301 Hervé Philippe and Patrick Forterre, "The Rooting of the Universal Tree of Life is Not Reliable," Journal of Molecular Evolution, vol 49, 1999, p. 510.
302 James Lake, Ravi Jain ve Maria Rivera, "Mix and Match in the Tree of Life," Science, vol. 283, 1999, p. 2027.
303 Carl Woese, "The Universel Ancestor," Proceedings of the National Academy of Sciences, USA, 95, (1998) p. 6854.
304 Elizabeth Pennisi, "Is It Time to Uproot the Tree of Life?" Science, vol. 284, no. 5418, 21 May 1999, p. 1305.
305 Jonathan Wells, Icons of Evolution, Regnery Publishing, 2000, p. 51..