"..... how to respond to the argument that some endogenous retroviruses (ERVs) seem to match the standard phylogeny of higher primates, supporting common descent. Endogenous retroviruses are thought to be parasitic junk sequences in our genome that were derived from viral DNA. Evolutionists often cite them as supposed evidence of common ancestry.
ERVs are a favorite with Darwin defenders -- so much so that one particularly uncivil activist, Abbie Smith, even named her popular science blog after them, "ERV."
In response,... when analyzing common descent, the number of ERVs shared by humans and chimps is beginning to look like it's not a very important question. An assumption in the question (and in the arguments from supporters of common ancestry) is that ERVs are a type of functionless "junk" DNA. Thus if apes and humans share ERVs in the same position in our genomes, that would seemingly count as evidence for common descent. But what if ERVs aren't junk?
What if they are a type of functional DNA? If that's the case, then shared ERVs could easily be explained by common design rather than common descent, and they would certainly no longer be some kind of special argument for common ancestry.
In fact there is good evidence that ERVs as a class of DNA are functional. A 2013 paper in PLOS Genetics using ENCODE data reported that very high percentages of endogenous retroviruses in the human genome are associated with open chromatin -- strong evidence of transcription -- and that they are transcribed non-randomly, suggesting some functional role:
Worse, their approach ignores the specific empirical evidence raised in the PLOS Genetics paper, which shows ERVs aren't merely transcribed -- they are transcribed in a non-random, enriched, cell type-specific manner that correlates with the transcription of other functional genetic elements. This is the opposite of random or stochastic transcription and it strongly suggests function.
.. ENCODE shows transcription isn't random:
ERVs are a favorite with Darwin defenders -- so much so that one particularly uncivil activist, Abbie Smith, even named her popular science blog after them, "ERV."
In response,... when analyzing common descent, the number of ERVs shared by humans and chimps is beginning to look like it's not a very important question. An assumption in the question (and in the arguments from supporters of common ancestry) is that ERVs are a type of functionless "junk" DNA. Thus if apes and humans share ERVs in the same position in our genomes, that would seemingly count as evidence for common descent. But what if ERVs aren't junk?
In fact there is good evidence that ERVs as a class of DNA are functional. A 2013 paper in PLOS Genetics using ENCODE data reported that very high percentages of endogenous retroviruses in the human genome are associated with open chromatin -- strong evidence of transcription -- and that they are transcribed non-randomly, suggesting some functional role:
Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized...We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily-transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation...these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.Again, we see from this that a great number of ERVs are found within open chromatin, strongly suggesting they are transcribed into RNA. Junk-DNA advocates respond that this isn't enough to show function because the transcribed DNA might just be producing "junk RNA." That's a weak rebuttal. As the paper states, ERV-based RNA was produced "in a cell type-specific manner" and was "associated with cell type-specific expression of neighboring genes." They further report "Thousands of LTR/ERV sequences are activated in a cell type-specific manner" and ERV transcription is highly enriched compared to other parts of the genome:
(Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque, "The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements," PLOS Genetics (May 9, 2013) (emphases added).)
Worse, their approach ignores the specific empirical evidence raised in the PLOS Genetics paper, which shows ERVs aren't merely transcribed -- they are transcribed in a non-random, enriched, cell type-specific manner that correlates with the transcription of other functional genetic elements. This is the opposite of random or stochastic transcription and it strongly suggests function.
.. ENCODE shows transcription isn't random:
ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases.ERVs fit exactly the same pattern, strongly suggesting they are functional. If they are functional, then they don't provide any kind of special evidence for common ancestry, even if they do fit into a nested hierarchy. Here's my view --------
- (1) Shared functional biological similarity that fits a nested hierarchy (i.e., a treelike pattern): Explained equally well by common design or common descent.
- (2) Shared non-functional biological similarity that fits a nested hierarchy: All things being equal, best explained by common descent.
- (3) Shared functional similarity that doesn't fit a nested hierarchy: Best explained by common design.
And the LORD God planted a garden eastward in Eden;
and there he put the man
whom he had formed.
Genesis 2:8