Amoeba supports front-loading
by Krauze
A prediction of front-loading is genes required for multicellularity being discovered in unicellular organisms, and I have previously suggested looking at amoebae, one of the oldest eukaryotes. Over at Uncommon Descent, DaveScot mentions that the amoeba Dictyostelium discoideum has had its genome sequenced. And that is good news for front-loading fans.
Although primarily unicellular, Dictyostelium has a novel approach to hardships: When starved, individual amoebae come together to form a multicellular fruiting body composed of a stalk with spores poised on top. So although some genes required for multicellularity were expected, the researchers behind the sequencing were nonetheless surprised by just how many such genes there were:
A broad survey of proteins required for multicellular development shows that Dictyostelium has retained cell adhesion and signalling modules normally associated exclusively with animals, whereas the structural elements of the fruiting body and terminally differentiated cells clearly derive from the control of cellulose deposition and metabolism now associated with plants.
When you are composed of several different cells, you need those cells to talk to each other. A cell in the eye should behave differently than a cell in the liver, and you better hope that each cell knows how it is supposed to behave. To ensure this, animals have a number of signalling molecules, called G-protein-coupled surface receptors. When the Dictyostelium genome was sequenced, researchers discovered the genes for 48 such receptors, divided into four gene families. This was surprising, as three of those families "had been thought to be specific to animals."
Having a receptor on your cell surface only ensures that you can receive messages, though. To process the information, you need intracellular regulation mechanisms, so that a cell in the eye can activate the genes that are required to make an eye. In Dictyostelium, three genes required for such a mechanism was found, one of which has the name Cbl. "This is entirely unexpected," note the researchers, "because it is the first time that a Cbl homologue has been observed outside the animal kingdom."
As a multicellular organism, you want to keep it together. To be more specific, you want to have some adhesion proteins binding your cells together, to prevent you from dissolving like a giant Slurpee. These genes were also found in the amoeba, prompting the researchers to write that "Dictyostelium uses a surprising number of components that have been normally only associated with animals."
The above observations confirm what I said in the beginning of this post: The amoeba Dictyostelium discoideum is good news for fans of front-loading. But there is one catch. One of the reasons why amoebae would be good candidates for front-loading is because they are an ancient group of organisms, and thus closest to the original designed cells. But one of the discoveries that fell out of the sequencing of Dictyostelium was that this species was closer related to multicellular organisms than previously assumed.
The further from the trunk a lineage is, the bigger the possibility that what we are seeing evolved after the original design event, and does not represent any front-loading. So although the findings from Dictyostelium are consistent with what we would expect from front-loading, it would have been nicer if we had made these findings in an older organism.
To some, this glass is half empty. I see it as half full: The opportunity still exists for a curious researcher with an eye for front-loading to find a more suiting organism and look for more good news.
References
Eichinger L., et al., "The genome of the social amoeba Dictyostelium discoideum", Nature 435(7038):43-57 (2005)
January 31st, 2007 at 7:08 pm
Hi Krauze,
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.
Comment by keiths — January 31, 2007 @ 7:08 pm
January 31st, 2007 at 7:29 pm
Any particular reason why the social amoeba isn't placed in the position presently labeled "common ancestor" in the tree above?
Comment by DaveScot1 — January 31, 2007 @ 7:29 pm
January 31st, 2007 at 8:09 pm
It looks like amoeba, or something like it (probably a flagellate), gave rise to animals and fungi, not plants.
Comment by Guts — January 31, 2007 @ 8:09 pm
January 31st, 2007 at 8:11 pm
Is there anything in front-laoding that requires that all life had a single common ancestor? Presumably a designer working with a common code could make a few basic types of organisms.
Comment by jhudson — January 31, 2007 @ 8:11 pm
January 31st, 2007 at 8:18 pm
I think Mike and Krauze are arguing that several types of bacteria-like super "bugs" were seeded on the earth and gave rise to bacteria and eukaryotes, but don't quote me on it.
Comment by Guts — January 31, 2007 @ 8:18 pm
February 1st, 2007 at 8:42 am
Keith,
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:
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.
Comment by Krauze — February 1, 2007 @ 8:42 am
February 1st, 2007 at 11:52 am
Carl Woese does more than toy with the idea of more than one common ancestor. I usually qualify common ancestor by putting "one or a few" in front of it as in "one or a few common ancestors". That separates it from scientific creation claims of a plethora of "created kinds" but doesn't restrict you to a single common ancestor either as orthodox evolution teaches.
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.
Comment by DaveScot1 — February 1, 2007 @ 11:52 am
February 1st, 2007 at 12:15 pm
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.
Comment by jhudson — February 1, 2007 @ 12:15 pm
February 1st, 2007 at 3:50 pm
I'd recommend this for those interested ,where it is argued that the tree of life metaphor is inadequate because evidence is accumalating for lineages consisting of mosaics of genes being derived from different ancestors. He argues for a more appropriate metaphor "the web of life".
Comment by Guts — February 1, 2007 @ 3:50 pm
February 1st, 2007 at 6:35 pm
Hi Jack,
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.
Comment by Krauze — February 1, 2007 @ 6:35 pm