The paper you mention is interesting. That bacteria are reduced eukaryotes is one message you can take away from it. Another message comes from the actual data that the authors used to support this claim. They draw on Hartman's and Federov's work on eukaryotic signature proteins (ESPs) - that is, proteins that are widespread in eukaryotes but with no homologs in prokaryotes. Even using very generous assumptions, Hartman and Federov still identified over 300 such ESPs. To me, a much more straight-forward interpretation of this is that eukaryotes and bacteria have separate ancestries, but then again, I'm just an IDiot.

It seems we have three quite different scenarios on our hands: Bacteria-as-reduced-eukaryotes, Woese's and Doolittle's "web of life", and my preferred scenario, where eukaryotes and bacteria have separate ancestries.

Starting from the beginning, the view of bacteria as reduced eukaryotes is easily compatible with front-loading seen in isolation, but I'm wary of it for other reasons. For one, bacteria aren't simply stripped-down eukaryotes. When it comes to metabolism, they have a wide set of strategies that eukaryotes can only dream of (eukaryotes have tapped into some of this diversity by incorporating the once free-living mitochondria and chloroplasts into their own cells). And there's also the bacterial flagellum. If this was designed, the first eukaryote must have had a copy. So why do modern eukaryotes use cilia for propulsion? My hunch is that if someone were to survey bacterial signature proteins, they could argue the other way around; that eukaryotes are stripped-down bacteria.

Then we have Woese and Doolittle rejecting the metaphor of the "tree of life" in favor of one where organisms exchange genes with such a promiscuous rate that lineages coalesce into a "web of life". I'm not a big fan of that view either. Individual genes function within the context of the whole cell, and bacteria and eukaryotes seem to have different kinds of architecture. Mike gave a http://www.thedesignmatrix.com... " rel="nofollow">good illustration of this, pointing to a eukaryotic protein that failed to fold up in a bacterial cell. Obviously, some horizontal gene transfer has taken place between bacteria and eukaryotes, just like some programs can run on both a PC and a Mac. But the kind of transfer envisaged by Woese and Doolittle isn't something I see as credible.

For these reasons, I favor the view of bacteria and eukaryotes as having distinct ancestries. There has most likely been some horizontal transfer between the two "kinds", but in the words of http://biology.plosjournals.or... " rel="nofollow">Ge, Wang, and Kim, this is just cobwebs on the tree of life, not something that eradicate the identities of the branches. Rather than one ur-eukaryote and ur-bacterium, there has probably been a diverse population of both cell types, which may account for some of the discrepancies between phylogenies constructed from different genes.

No, there's nothing in front-laoding that requires that all life had a single common ancestor. In fact, as Guts points out, Mike and I are toying with the idea of bacteria and eukaryotes having separate ancestries.

That would be interesting to see.

I read a paper a while back that discussed the evidence that prokaryotes are actually derived from eukaryotes via "sequence loss and cellular simplification"; this would seem to track conceptually with front-loading from a common ancestor.

One thought; I wonder if such a tree could really be produced even from a common ancestor. Assuming there was even one very genetically diverse ancestor, it would quickly proliferate and that group would be hard to distinguish from multiple similar ancestors.

Indeed, the above mentioned mechanism of "sequence loss and cellular simplification" would seem to be the primary modus operandi of natural selection on a front-loaded ancestor - in which case a tree might not be the best representation of the development of genetic diversity, but natural selection would seem to act like a series of filters on a genetic spectrum. Indeed, a recent study indicates that the TOL is a poor assumption and suggests "pattern pluralism" instead.

As such, we wouldn't necessarily consider that the amoeba genome was "further from the trunk" but rather subject to a different set of selection filters and only gives us one snapshot of the whole picture of an original, more diverse genetic ancestor, which no living organism can fully represent.

But I'm just blabbering, I'm sure you folks have thought of all these things. I appreciate your work here.

I lean towards "created kinds" being front loaded in schematic form into one or a few genomes when life was first placed on this planet. The end goal of the front loaded evolution is to produce a technological species who can discover and seed other suitable planets with life and thus keep the cycle of life going ad infinitum. When you think about it that requires reaching some critical milestones such as an oxgenated atmosphere to support land-based life with rapid metabolisms and then laying down a supply hydrocarbon fuels to power an industrial civilization (which also requires atmospheric oxygen to support burning those fuels).

We seem to be right on track and getting close to the goal. Our next generation telescopes are designed to detect earth-size planets around other stars and collect enough light from them for spectroscopic analysis while the Voyager I spacecraft recently became the first manmade object to leave the solar system. Another hundred years of progress should be all it takes to accomplish our mission of reproducing our form of organic life on a different planet around a younger star. Then we might be in trouble because if life follows the normal course… the parent dies after it successfully reproduces.

As I also said in my post, it isn't merely about Dictyostelium having multicellular genes, but also the number of genes thought to have been unique to animals.

Dave,

The researchers write:

Using morphological criteria, early workers were unsure whether to classify Dictyostelids as fungi or protozoa. Molecular methods indicated that they were amoebozoa and also suggested that Dictyostelium diverged from the line leading to animals at about the same time as plants. A study of more than 100 proteins suggested that Dictyostelium diverged after the plant-animal split, but before the divergence of the fungi. The recent finding of a gene fusion encoding three pyrimidine biosynthetic enzymes, shared only by Dictyostelium, fungi andMetazoa, indicates that the amoebozoa are a true sister group of the fungi and Metazoa. [References omitted]

Jack,

No, there's nothing in front-laoding that requires that all life had a single common ancestor. In fact, as Guts points out, Mike and I are toying with the idea of bacteria and eukaryotes having separate ancestries.

Most, if not all, neo-Darwinians believe that colonial forms of life were the immediate predecessors of true metazoa. Given that, I'm finding it hard to understand why you think genes for multicellularity in Dictyostelium constitute evidence for front-loading.

I would get more excited if these genes were found in non-colonial organisms.