Unique “Orphan Genes” Are Widespread; Have No Evolutionary Explanation

We often hear about the similarities between genomes, but what about the differences?  There’s a growing realization that groups of animals have genetic orphans – genes that are unique to that line (see 01/02/2003).  These genes have no evolutionary homology or kinship to genes from other lineages.  How did they arise?  And what do they do?

A German team examined orphan genes, also called “taxonomically restricted genes” (TRGs) in two species of hydra.  They found that the hydra-specific Hym301 genes do something: they affect tentacle formation.  Knockout experiments and alteration of expression of Hym301 genes clearly caused changes in tentacle length and arrangement.  Their work was published in PLoS Biology¹ and was summarized by Science Daily.  They felt their experiments demonstrate that orphan genes are not baggage but are involved in the specific morphological character of the organism.

How do orphan genes arise?  Their explanation was hidden in a passive-voice verb that basically says it just happens: “Given that Hym301 genes are without homologs in eukaryotic genomes outside Hydrozoa, they might have been specifically acquired in this animal group.”  But how were they acquired, and who acquired them?  Their next sentence could not even ascribe the acquisition to natural selection: “An important step that remains to be demonstrated is the role of natural selection in fine tuning of expression of Hym301 genes or their gene regulators for this lineage-specific adaptation.”  If natural selection is only fine-tuning what was already there, it could not be responsible for the origin of Hym301.  This was the only mention of natural selection in the paper.

References to evolution in the paper were oblique, vague, and otherwise unhelpful for macroevolutionary theory.  For example,

• Understanding the molecular events that underlie the evolution of morphological diversity is a major challenge in biology.
• Our data indicate that novel genes may play a role in the creation of novel morphological features, thus representing one way how evolution works at the genus level.  Appearance of novel genes may reflect evolutionary processes that allow animals to adapt in the best way to changing environmental conditions and new habitats.
• Models for evolution of TRGs [taxon-restricted genes] have been proposed and the significance of their evolutionary contribution to ecological adaptation has been postulated.  Despite this, TRGs are poorly studied and little understood, in large part because the lack of homology confounds attempts to determine the putative function of the protein.
• Thus, although progress has been made towards understanding the molecular mechanisms controlling the evolution of morphology, many questions remain to be addressed: What genes are differentially expressed in two closely related species and how many?  Do the differences occur predominantly in structural or regulatory genes?  Do novel genes play a role in generation of morphological novelties?  And, ultimately, what is the genetic basis of species-specific morphologies?
• Our data show that morphological diversity at the genus level can be generated through changes in the spatial and temporal deployment of genes that are not highly conserved across long evolutionary distances.  We also propose that losses and duplications of those novel genes among closely related species may be one of the driving forces leading to morphological diversification in the genus Hydra.
• So far, the evolutionary significance of TRGs has not been widely recognized.
• The data provide experimental support for the hypothesis that novel genes are involved in specific ecological adaptations that change over time and that such genes serve as the raw material for microevolutionary divergence.
• The observations show that regulatory evolution may act not only by modifying expression domains of conserved genes, but also by spatial and temporal changes in the deployment of TRGs, and that TRGs can be integrated with conserved developmental regulators to form functional signaling cascades.
• Therefore, future research on these species may provide novel insights on how TRGs are involved in the evolution of the corresponding adaptive traits.  Although it is difficult to generalize from this example, comparing morphogenetic processes in different Hydra species seems to promise new perspectives on how nature fine-tunes morphogenesis [the origin of body plans].  Discovering not only the similarities but also the molecular differences between different organisms might yield intriguing clues in the mechanisms responsible for evolutionary changes.

But again, they did not say where the TRGs come from.  If evolution deploys them for microevolutionary fine-tuning within genera, that still does not explain how they arrived in the first place.  Our online book shows that complex genes cannot be expected to pop into existence by chance.
Maybe this is just a little problem for Darwin, though – if orphan genes are very rare.  How common are they?  The author’s summary states that “every group of animals also has a small proportion of genes that are extremely variable among closely related species or even unique.”  They elaborated on that “small proportion” in paragraph two: it is a “substantial fraction” of the genome –

There is, however, one much less appreciated source for the creation of morphological novelties.  All genome and expressed sequence tag (EST) projects to date in every taxonomic group studied so far have uncovered a substantial fraction of genes that are without known homologs.  These “orphans” or “taxonomically restricted genes” (TRGs) are defined as being exclusively restricted to a particular taxonomic group.  For example, analysis of the phylum Nematoda [roundworms] has identified more than 20% of genes that were nematode-unique TRGs.  The draft genome of Ciona intestinalis revealed that nearly one-fifth of the genes were orphans.  A comparison between the genome sequences of Schizosaccharomyces pombe and Saccharomyces cerevisiae [yeast] showed about 14% of the predicted proteins to be unique to Sc. pombe and 19% unique to Sa. cerevisiae.  In Drosophila, [fruit fly] TRGs include indispensable regulators of development such as bicoid and spatzle.  Recent comparative data on the genomes of 12 Drosophila species revealed that about 2.5% of genes are not present outside of the genus Drosophila and, therefore, have most likely arisen de novo.  An even larger proportion of lineage-specific genes have been detected in the genome of Tribolium [a beetle].  In bacteria, the cumulative number of orphans identified does not appear to be leveling off, although hundreds of complete genome sequences have been already analyzed.

The authors gave no suggestion that these orphan genes developed from precursors by an evolutionary process.  Notice, for instance, this sentence about TRGs: “Their functions and origins are often obscure,” and later, “Therefore, we consider the members of the Hym301 family as TRGs, which have most likely originated within the class Hydrozoa and expanded in the genus Hydra.”  The phrase most likely originated is silent on the question of how, and from where.  A similar dodge phrase is have arisen, as illustrated in the final Discussion section: “The sequencing of a large number of eukaryotic and bacterial genomes has uncovered an abundance of genes without homologs, classified as TRGs and has shown that new genes have arisen in the genomes of every group of organisms studied so far including humans.”  Their experiments provide no clues about where these genes came from.

Again, they said, “The observations also extend earlier findings of an abundance of TRGs in organisms from prokaryotes to animals.”
The question of the origin of orphan genes was left to others: “Therefore, future research on these species may provide novel insights on how TRGs are involved in the evolution of the corresponding adaptive traits…. Discovering not only the similarities but also the molecular differences between different organisms might yield intriguing clues in the mechanisms responsible for evolutionary changes.”  Science Daily was no help, either.  The article also just hoped that the finding will be “pointing the way to a new, more complete understanding of how evolution works at the level of a particular group of animals.”  It concluded, “Emergence of ‘novel’ genes may reflect evolutionary processes which allow animals to adapt in the best way to changing environmental conditions and new habitats.”  But how does evolution explain emergence?  Stuff happens?

1.  Khalturin, Anton-Erxleben, Sassman, Wittlieb, Hemmrich and Bosch, “A Novel Gene Family Controls Species-Specific Morphological Traits in Hydra,” Public Library of Science Biology, Vol. 6, No. 11, e278 doi:10.1371/journal.pbio.0060278.

If you are not yet convinced that evolutionary theory is a mishmash of bluffing and obfuscation, in which scientists play mind games with word games, then please read this paper and explain how evolution was of any help at all in understanding this phenomenon.  While they were busy finding homologies (good grief, even these authors referred to Darwin’s finches), a major obstacle to evolution was right there in front of them, but they ignored it: orphan genes are “poorly studied and little understood,” they said.  Well, go study them, for crying out loud!  Here is a finding that amounts to falsification of Darwinism and confirmation of creationism (limited variation within created kinds), and these authors tiptoed around the bad news with carefully-crafted passive verbs built on the assumption that evolution might explain it somehow, provided you are willing to wait for the vaporware and futureware that is perpetually on back order.  “Their functions and origins are often obscure,” we are told.  They “emerged” somehow.  We need an emerge-ncy end to obscur-antism.

Their passive verbs most likely originated, have arisen and might have been acquired are nothing more than appeals to miracles.  Our online book shows that the chance origin of genes and proteins cannot happen, and will not happen, any time or place in this universe or any other.  The miracle of creation seems almost natural by comparison.  Evolutionary theory needs to declare chapter 7 bankruptcy, because no scientific bailout is forthcoming.  The creationist creditors, who founded modern science, want their assets back.