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Explore Evolution wrongly state that biologists originally maintained that the genetic code is absolutely universal (invariant); that this absolute universality was considered evidence for common descent; that this would be a reasonable inference because changing the code would be invariably lethal ("not survivable"); and finally, that the claim of universality fell apart in the 1980s with the discovery of variant genetic codes.
Knight RD, Freeland SJ, Landweber LF. Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet. 2001; 2:49-58,
Explore Evolution claims that the common ancestry of life is disputed because:
Explore Evolution claims that certain scientists dispute the existence of a single universal ancestor, citing authors would not actually dispute universal common descent. They just disagree about the form it took, and the nature of the population of organisms from which modern living things evolved.
Explore Evolution claims:
Explore Evolution's arguments against molecular clocks are a bungled mishmash of actual facts, misinterpretations and completely spurious claims. First, the authors raise the issue of calibration of the molecular clock. This is an acknowledged potential problem in using the clock to date certain evolutionary events, especially those in the very deep past. Nevertheless, when appropriate methodology and controls are used, molecular clock dating has been shown to be reliable and consistent.
The authors do not understand phylogeny, and have a very limited understanding of the biological vocabular and issues. They propose that if common descent is correct, then:
A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).
This is simply wrong.
Phylogenetic trees based on single genes (or small numbers of genes) can differ from one another, but Explore Evolution overstates both the extent of the inconsistencies and their implications for phylogenetic reconstruction. Inconsistencies are most common when analyzing phylogenetic events in the very deep past (such as separation of the main animal groups in the pre-Cambrian), and occur for reasons that are well characterized and indeed predicted based on statistical and evolutionary considerations (changes in evolutionary rates, convergent evolution, etc.).
The 3 Domains
Page 23 is a sidebar showing "Biological Classification." The page correctly points out that the most fundamental taxonomic split of organisms is into the three domains: Bacteria, Archaea, Eukaryota. Of these domains, Explore Evolution says, "Each of these has a fundamentally different cell structure."