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A frequently heard phrase in discussions of the science of origins is "evidence-based". It is important that scientists affirm that their work has to do with evidence and that it is different from speculation. This blog is concerned with the evidence base for evolutionary innovation via gene duplication. The press release for the paper under consideration claims that the researchers have come up with answers, but it also contains a significant acknowledgement that, in the past, there have been significant unanswered questions about this topic:

"An important unanswered question in Darwin's theory of evolution is how new characteristics seem to appear out of nowhere. Such innovations appear to contradict the principle of gradual change, in which existing characteristics slowly evolve into another form. Yet we know that many "inventions" took place during the evolution of life."

"These results provide answers to an argument frequently used by opponents of the theory of evolution: the chance of the occurrence of a new characteristic - a functional new segment of DNA - from scratch is similar to the chance of a modern jumbo jet assembling spontaneously from a few pieces of scrap metal." (Sources - text and graphic)

The scientists consider that they have succeeded in rebuilding the DNA and proteins of prehistoric yeast cells. This is what they say:

Steven Maere: "We used sequence reconstruction algorithms to predict the DNA sequence of ancestral genes from dozens of present-day DNA sequences. This enabled us to rebuild the corresponding ancestral proteins."
Karin Voordeckers: "We searched very specifically for how the yeast adapted to break down various sources of sugar. We found that the primal gene that codes for the protein for the digestion of maltose - a sugar in grain - was copied a number of times during evolution. The DNA of some copies changed slightly, resulting in new proteins that could break down different sugars. By modeling these changes in the corresponding proteins, we now understand how just a few changes in the DNA can lead to the development of new activity in the corresponding proteins"
The scientists think that this type of duplication of the DNA often forms the basis of the emergence of apparently "new" proteins. In other words: the jumbo jet is gradually built from a copy of an existing airplane.

In a blog on the research, Doug Axe finds that the paper does not explain the origin of anything new. He suggests that the authors have used the word "Innovation" in their title in an "innovative" way!

"They clearly want to say that they've shown how a bunch of brand new enzyme activities can evolve from an ancestral enzyme that lacks them. I understand their passion. That's what I'd want to say if I wanted Darwinism to be true. And, truth be told, science papers do allow authors to cast their results in their own terms. But they also press them to state the facts plainly, and in this case here's the plain statement:
"The preduplication [i.e., ancestral] ancMalS enzyme was multifunctional and already contained the different activities found in the postduplication [i.e., evolved] enzymes, albeit at a lower level."
So, all we have here is a demonstration of what we already knew -- that evolution can adjust somewhat the relative preferences enzymes show for the molecules they already work on. Those aren't new activities, though, and this isn't a new result either."

Axe is reminding us that the evidence base says "complexity comes from complexity", which should be regarded as the finding of science. Those who seek to build complexity gradually from simple precursors are still presuming the answers rather than discovering them. The words quoted above: "Yet we know that many "inventions" took place during the evolution of life" is stating a 'given' of evolutionary theory and is unwilling to even consider that the evidence points elsewhere.

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
Karin Voordeckers, Chris A. Brown, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere, Kevin J. Verstrepen
PLoS Biology, 10(12): e1001446 | doi:10.1371/journal.pbio.1001446

Abstract: Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Blog:

Belgian Waffle by Douglas Axe (Biologic Institute, 17 January 2013)