American, British and Canadian biologists have sequenced a newly discovered giant marine virus designated Cafeteria roenbergensis virus (CroV). It has a double-stranded DNA genome of ~730 kb, with 544 predicted protein-coding genes. Half of these have no match among sequenced genomes (see pie-chart), but many others have various apparent functions among higher life forms:

"The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy-d-manno-octulosonate, a key component of the outer membrane in Gram-negative bacteria."

All of this is unsurprising if viruses are primary agents for horizontal gene transfer (HGT), and if HGT is essential for evolutionary progress, as we believe.

Phylogenetic tree of vertebrates with branches leading to human and to mouse marked as orange line.... Panels A and B show the assignments of new genes to branches on the phylogeny of human and mouse, respectively. The young genes, those primate- and rodent-specific, are marked with pink boxes. The notation with two numbers separated by a colon indicates the branch assignment and number of genes occurring in the given branch. For example, in the human lineage represented in panel A, in branch 12: 389 genes originated after the split of humans and chimps.... doi:10.1371/journal.pbio.1000494.g001

This team begins by identifying 1,828 human genes that are primate specific, and 3,111 mouse genes that are rodent-specific, calling them all "young genes". They then divide the young genes into three sub-categories, "DNA-level duplicates, RNA-level duplicates (retrogenes), and de novo genes." We note that genes in the first two sub-categories, the duplicates, come from pre-existing sequences. Thus, any programmatic content in these genes is not "new".

What about the de novo ones? According to the report, these genes have no annotated paralogs and no matches in existing databases. Darwinian theory gives no account of them. Such an account would show how their programmatic content was composed, step-by-step. Instead, they appear to have come, virtually finished, from nowhere.

Genes that are older than the features they encode and genes that come from nowhere, both are confounding for darwinism, because both acquired their programmatic content without the apparent benefit of mutation-and-selection. In cosmic ancestry, however, all genes are very old. The ones that seem to come from nowhere are merely being noticed for the first time.

We sincerely invite any pointers to counterexamples: If darwinian mutation-and-selection composes new genetic programs, where's the evidence?

The two biologists mention a possibility: "These genes could be found in the yeast genome as a result of more recent lateral gene transfer (LGT), rather than being a relict of mitochondrial endosymbiosis." And they conclude, "Only half of eukaryotic genes have an identifiable prokaryotic homolog.... It is remarkable that some of the original partners' contributions might have persisted for > 1 billion years of evolution.... Yeast metabolism, and presumably eukaryotic metabolism in general, is a complex tapestry of prokaryotic threads and eukaryotic innovations."

Many eukaryotic genes have no known predecessors or homologs anywhere. This situation does not support the darwinian scheme, whereunder genes are composed gradually, by trial and error. Genes composed that way would leave a descending trail of identifiable precursors, but there seems to be no such trail. Instead, the genes are either present or absent, as observed here. That the innovations were composed by the darwinian method is supported only "presumably". Meanwhile, this research supports our hypothesis that all genes are very old "threads" that must be acquired, either vertically... or otherwise.

Figure 3. Origin of protein-coding genes from scratch. New coding regions may emerge de novo from noncoding genomic sequences. First, proto-open reading frames (proto-ORFs; thin blue bars) acquire mutations (point substitutions, insertions/deletions; yellow stars) that remove, bit by bit, frame-disrupting nucleotides (red wedges). Transcriptional activation of ORFs (through acquisition of promoters located in the 5' flanking region) encoding proteins with potentially useful functions may allow for the evolution of novel protein-coding genes. (Large blue box) Functional exon, (pink right-angled arrow) TSS, (transparent pink box) untranslated 5' sequence. Note that the transcriptional activation step may, alternatively, also precede the formation of complete functionally relevant ORFs. Figure and caption from Kaessmann, 2010.

Our analysis begins with Kaessmann's summary of the ways new genes have originated —
1 "...new genes have arisen from copies of old ones...."
2 "...protein and RNA genes were composed from scratch...."
3 "...protein-coding genes metamorphosed into RNA genes...."
4 "...parasitic genome sequences were domesticated...."
5 "...the resulting components also readily mixed to yield new chimeric genes...."

We note that methods 1, 3 and 4 describe genes whose sequences are preexisting, needing only to be activated and optimized within limited ranges. Method 5 describes the assembly of genes from major pieces. Only method 2 looks like it would support strict darwinism. Let's look at it more closely.

The section titled "Gene origination from scratch" states, "In other words, new genes arise from previously nonfunctional genomic sequence, unrelated to any preexisting genic material (Fig. 3)." Already, new genes are seen come from pre-existing material, whose "origin" is unexplained. This section continues:

"The de novo origin of entire protein-coding genes was long considered to be highly unlikely. For instance... François Jacob noted in an influential essay that the 'probability that a functional protein would appear de novo by random association of amino acids is practically zero' and that therefore the 'creation of entirely new nucleotide sequence could not be of any importance in the production of new information' (Jacob 1977)."

"In spite of these notions, recent work has uncovered a number of new protein-coding genes that apparently arose from previously noncoding (and nonrepetitive) DNA sequences. Probably the first such case described in the literature is presented by the morpheus gene family that emerged in an Old World primate ancestor (Johnson et al. 2001). Although the details regarding the emergence of the original coding sequence remain unclear, the lack of any corresponding orthologous sequences outside of Old World primates suggest a de novo origin for this gene family...." Stepwise composition gets no support here. The sequence has no identifiable source.

"Other studies have followed suit and have provided a more detailed picture of de novo gene origination. For example, 14 de novo-originated genes have been identified in Drosophila (Levine et al. 2006; Zhou et al. 2008)...." We analysed those reports when they were current, finding poor evidence for stepwise composition. Links are below.

"For example, Knowles and McLysaght (2009) recently identified three genes that seem to have arisen from scratch on the human lineage. Detailed analyses of these human-specific genes, which involved comparisons with corresponding noncoding sequences from closely related primate relatives, revealed that a few mutational events after the separation of the human and chimpanzee lineages abolished 'disabling' nucleotides in the ancestral open reading frame precursors (Fig. 3 [above]), allowing relatively long coding sequences to emanate in humans. Importantly, the functionality of these new human genes is supported by evidence for translation of their coding sequences...." The figure shows a precursor gene apparently 95% composed, needing only 2 point mutations to restore the ORF. Deeper analyis is available on our webpage "Three New Human Genes," posted a year ago, linked below.

We think this review of the origins of new genes, purporting to sustain the darwinian account of them, fails. We think a similar failure is quite common in darwinists' writings. We wish that instances of this failure were noticed and discussed openly. Moreover, we think the cited evidence, and lots more, points instead to genes that are supplied, preexisting, whole or in major pieces — which darwinism cannot explain, but which cosmic ancestry requires.