The paper I cited describes the structural similarities between ubiquitin and its prokaryotic homologs.
This one fold seems to have been conserved. The rest, not so much. The function of the proteins, not at all.
Yet it is the basic structure of a protein that determines its function - along with the proteins it interacts with, of course. My point is that loading the first genomes with an ubiquitin-related fold allows it to be easily co-opted into the role used by eukaryotes.
I wasn't suggesting that the frontloaders would load only eukaryotes. The more, the merrier, and the higher the chances of metazoa.
The last point doesn't really fit very well with the first two, does it? It would also mean that, far from frontloading a prokaryote LUCA with eukaryotes in mind, the frontloaders (FLs) would presumably have had terraforming prokaryotes in mind when designing their eukaryote LUCA. Why not make sure by designing the proks as well? The more, the merrier, and the better the chances.....
Quite right. I personally favor the hypothesis that the LUCA was prokaryotic, and not eukaryotic, although some researchers say that the LUCA was more of a eukaryote precisely because of its complexity and the large number of proteins its genome encoded. This is fully compatible with front-loading.
Why wouldn't the "logic of frontloading" predict actual ubiquitin in the proks?
Because the mutations do happen, and over deep time, a protein sequence can change quite extensively - to the point that it is no longer the original protein (but structurally similar, nonetheless, and this is what matters).
There's also a problem here that Mr. Jack hinted at in a post above. Ubiquitin being ubiquitous in eukaryotes does not necessarily mean that it's necessary for metazoa, or that the fold is necessary. It could just be a "frozen accident".
The universal distribution of ubiquitin among eukaryotes strongly implies that it is necessary for eukaryotic existence, does it not? True, it could be a "frozen accident." But the front-loaders aren't going to gamble their chances on accidents. It would be far better design logic just to put that protein fold into the first cells.
Quite right. If the intent was for metazoans to arise in the future, why not make them straight away?
Metazoans don't survive that well in an environment like that of the early, hostile earth ya know.
Do you want oxygen in the atmosphere? Dump some genetically modified algae into the planet's oceans.
Alternatively, you could put some cyanobacteria into the planet's oceans. That's why terra-forming is intimately linked with front-loading. In order to ensure that animals and plants can arrive on the scene later, you have to change the earth such that it is hospitable to animals and plants.
How did you determine that ubiquitin structure was intended for use in metazoans? How did you rule out the possibility that other proteins were destined for this role, but evolution caused ubiquitin to fill this role instead.
That's not really the issue IMHO. If we assume, for sake of argument, that the Metazoa we see today was the intended outcome of a front-loading scheme, we can make testable predictions regarding biotic reality. This is the point. Confirmation of those predictions strengthens the above thesis.
Now, you might rightly ask why we should assume that Metazoa were the intended outcome of front-loading, instead of, say, a race of flying spaghetti monsters. But here is where fallible intuition comes into play. If we were to seed another planet with life, and front-load objectives into existence, we would likely choose plants and animals. This, of course, is not evidence that Metazoa were the intended outcome of front-loading - I am well aware of that. However, if we follow the line of thought that Metazoa were, in fact, the intended outcome of front-loading, from here we can make real predictions that are not made by the non-teleological model. The non-telic view of life does not require that prokaryotes have ubiquitin homologs. Darwinian evolution has been very comfortable with the fact that, prior to structural analyses, there were no known prokaryotic homologs of ubiquitin. Yet front-loading predicts exactly this.