Editing Common descent (section)

==Objections==

[[File:Tree Of Life (with horizontal gene transfer).svg|class=skin-invert-image|thumb|2005 [[tree of life (biology)|tree of life]] shows many [[horizontal gene transfer]]s, implying multiple possible origins.]]

===Gene exchange clouds phylogenetic analysis===
{{further|Horizontal gene transfer}}

Theobald noted that substantial [[horizontal gene transfer]] could have occurred during early evolution. Bacteria today remain capable of gene exchange between distantly-related lineages. This weakens the basic assumption of phylogenetic analysis, that similarity of genomes implies common ancestry, because sufficient gene exchange would allow lineages to share much of their genome whether or not they [[monophyly|shared an ancestor (monophyly)]]. This has led to questions about the single ancestry of life.<ref name="theobald" /> However, biologists consider it very unlikely that completely unrelated proto-organisms could have exchanged genes, as their different coding mechanisms would have resulted only in garble rather than functioning systems. Later, however, many organisms all derived from a single ancestor could readily have shared genes that all worked in the same way, and it appears that they have.<ref name="theobald" />

===Convergent evolution===
{{further|Convergent evolution}}

If early organisms had been driven by the same environmental conditions to [[Convergent evolution|evolve similar biochemistry convergently]], they might independently have acquired similar genetic sequences. Theobald's "formal test" was accordingly criticised by Takahiro Yonezawa and colleagues<ref>{{cite journal |last1=Yonezawa |first1=Takahiro |last2=Hasegawa |first2=Masami |title=Was the universal common ancestry proved? |date=16 December 2010 |journal=Nature |volume=468 |issue=7326 |page=E9 |doi=10.1038/nature09482 |pmid=21164432|bibcode=2010Natur.468E...9Y |s2cid=4318346 |doi-access=free }}</ref> for not including consideration of convergence. They argued that Theobald's test was insufficient to distinguish between the competing hypotheses. Theobald has defended his method against this claim, arguing that his tests distinguish between phylogenetic structure and mere sequence similarity. Therefore, Theobald argued, his results show that "real universally [[Conserved sequence|conserved]] proteins are [[sequence homology|homologous]]."<ref>{{cite journal |last=Theobald |first=Douglas L. |date=16 December 2010 |title=Theobald reply |journal=Nature |volume=468 |issue=7326 |page=E10 |doi=10.1038/nature09483|bibcode=2010Natur.468E..10T |s2cid=4317014 |doi-access=free }}</ref><ref>{{cite journal |last=Theobald |first=Douglas L. |date=24 November 2011 |title=On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence |journal=Biology Direct |volume=6 |issue=1 |page=60 |doi=10.1186/1745-6150-6-60 |pmc=3314578 |pmid=22114984 |doi-access=free }}</ref>

===RNA world===
{{main|RNA world}}
The possibility is mentioned, above, that all living organisms may be descended from an original single-celled organism with a [[DNA]] [[genome]], and that this implies a single origin for life.  Although such a universal common ancestor may have existed, such a complex entity is unlikely to have arisen spontaneously from non-life and thus a cell with a DNA genome cannot reasonably be regarded as the origin of life.  To understand the origin of life, it has been proposed that DNA based cellular life descended from relatively simple pre-cellular self-replicating [[RNA]] molecules able to undergo [[natural selection]].   During the course of evolution, this RNA world was replaced by the evolutionary emergence of the DNA world. A world of independently self-replicating RNA genomes apparently no longer exists (RNA viruses are dependent on host cells with DNA genomes).  Because the RNA world is apparently gone, it is not clear how scientific evidence could be brought to bear on the question of whether there was a single origin of life event from which all life descended.