Literature

Since vertebrates have a spine, they are regarded as having a higher complexity. "Nonetheless, demonstrating this difference in morphological complexity is difficult, and determining its causal basis has proven even less tractable. Typically, causality has been sought in the phenomenon of genome duplication." There is a problem with this, as the authors explain: "However, the absence of any obvious increase in morphological complexity associated with other known genome duplication events (GDEs), especially within the actinopterygian fishes, suggests that the causal link between morphological complexity and GDEs is tenuous at best." Towards the end of their paper, they reject GDE completely as a plausible mechanism:

"Indeed, in contrast to the rhetoric, no good evidence has been marshaled in support of the much-vaunted hypothesis that GDEs can confer increasing organismal complexity."

To understand the argument of the research paper, it should be noted that the original model of protein formation within the cell was that DNA was first transcribed to RNA, and RNA was then translated to protein. Subsequently, there have been many modifications, all associated with control mechanisms. Many RNAs are non-coding and they do not make protein. These RNAs can be thought of as switch-like controls that regulate the formation of gene products.

"An alternative explanation for increasing morphological complexity has been increasing the complexity of gene regulatory networks. Although usually considered from the perspective of protein-coding genes, vertebrates are also distinguished from invertebrates by the transcribed, noncoding complements of their genome, with mammalian genomes transcribing over an order of magnitude more noncodingRNAas compared with either worm or fly. Importantly, it is among this noncoding sequence that a variety of new classes of regulatory factors has been discovered, including microRNAs (miRNAs), which has been postulated as developmental and evolutionary determinants of organismal complexity. Indeed, vertebrates possess many more miRNAs than any invertebrate sampled to date, and >50 new miRNA families are thought to have evolved in the vertebrate lineage sometime after its split from the invertebrate chordates and before the divergence of osteichthyan fishes."

The paper does establish a link between the emergence of many new miRNA families and vertebrate morphological complexity, and the authors ask whether this is a coincidence or whether there is causality. In their view, causality must be the answer.

"Of course, it could be argued that the correlation between miRNA acquisition and morphological complexity is exactly that, a simple correlation. However, we suggest otherwise given that many of these 41 miRNA families are expressed in vertebrate-specific cell types or tissues [. . .]. Given the role miRNAs play in the specification of cell and tissue types, we suggest that the origin of these cellular novelties was predicated on the origin and fixation of these novel miRNAs."

Alysha Heimberg summarises the situation thus: "There was an explosive increase in the number of new microRNAs added to the genome of vertebrates and this is unparalleled in evolutionary history." Co-author, Philip Donoghue adds: "Most of these new genes are required for the growth of organs that are unique to vertebrates, such as the liver, pancreas and brain. Therefore, the origin of vertebrates and the origin of these genes is no coincidence." The press release refers to the authors claiming "to have solved this scientific riddle".

The authors have established an association, but causation is a much stronger word. There are numerous gaps in the causal explanation as it stands.

"Such rapid rates of miRNA innovation, and the correlation with the dramatic increase in morphological complexity, beg the question of how and why this burst of miRNA family innovation occurred. The basis of miRNA innovation in animals is controversial as there are a number of competing, but weakly supported, hypotheses."

It is an understatement to say that how and why questions abound! We do not just have to consider miRNA innovation, but the introduction of miRNAs that deliver functionality. With the proposed rapid burst of changes, there are important questions about the viability of animals experiencing concurrent transformation of numerous regulatory networks. In the present state of knowledge, design-based explananations of causation cannot be dismissed except on ideological grounds. We have here a striking case of complex specified information, and that is the hallmark of designed systems.

It is worth noting, before concluding, that the initial reaction of many evolutionary biologists was to regard all non-coding DNA (including the sequences now known as miRNA) as junk. This is the context for understanding the headline of the EurekAlert report. This blog has drawn attention previously (here, here and here) to this cul-de-sac in the history of evolutionary thought.

MicroRNAs and the advent of vertebrate morphological complexity
Alysha M. Heimberg, Lorenzo F. Sempere, Vanessa N. Moy, Philip C. J. Donoghue and Kevin J. Peterson
Proceedings of the National Academy of Sciences, USA, February 11-15 2008.

Abstract: The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these ~22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show that 41 miRNA families evolved at the base of Vertebrata, as they are found and/or detected in lamprey, but not in either ascidians or amphioxus (or any other nonchordate taxon). When placed into temporal context, the rate of miRNA acquisition and the extent of phenotypic evolution are anomalously high early in vertebrate history, far outstripping any other episode in chordate evolution. The genomic position of miRNA paralogues in humans, together with gene trees incorporating lamprey orthologues, indicates that although GDEs can account for an increase in the diversity of miRNA family members, which occurred before the last common ancestor of all living vertebrates, GDEs cannot account for the origin of these novel families themselves. We hypothesize that lying behind the origin of vertebrate complexity is the dramatic expansion of the noncoding RNA inventory including miRNAs, rather than an increase in the protein-encoding inventory caused by GDEs.

See also:

Evolving complexity out of 'junk DNA', EurekAlert, 11 February 2008