Talk:Last universal common ancestor/Archives/2014/June

Still confusing with Ur-organism

//In 1998, Carl Woese proposed (1) that no individual organism can be considered a LUA, and (2) that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.[22] Although at first glance this claim seems to directly contradict Theobald's 2010 result, it does not. Both authors agree that life emerged only once. However, at the beginnings of life, ancestry was not as linear as is today because the genetic code took time to evolve.[23] Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. Thus Woese contends that the last universal ancestor was not a single cell but a distributed community (with a single point of origin) that collectively possessed the traits LUCA is theorized to have.//

With all due respect, I still think my fellow editors are confusing LUCA with the concept of an Ur-organism. Let's start with the difference between them.

The Ur-organism is the immediate product of organic class molecules assembling into a cell-like structure. Ur-organisms would lack, at the very least if not other features, the high-fidelity genetic replication and mutation proofreading of modern cells, which is why I call them cell-like structures.

The Last Universal Common Ancestor (LUCA) lived many generations after the time of the Ur-organisms. It was not the very first cell in the same way the Y-Chromosomal Adam was not the very first man, and the Mitochondrial Eve was not the very first woman. The difference is that this "Single-Celled Adam" is an ancestor to all surviving lineages of all living things, rather than just those of humans.

Was this microbial Adam a member of a larger Early Microbial Community? Yes, absolutely. What is so special about this individual cell within that community? Its progeny survived beyond the very early stages of prokaryotic evolution, and everybody else's lineages went extinct not too long after, perhaps within a thousand generations later if we're being very generous. That is what makes LUCA so special.

Almost certainly, there were multiple Ur-organisms. An overwhelming majority of them would have gone extinct quickly, their lineages already lost even at the times most of the Early Microbial Community would have lived. (Actually, consider how many Ur-organisms would have died off immediately after they formed, having no lineage to speak of at all.) Still, a small handful of them may have had distant progeny in LUCA's time.

The Genetic Code, along with at least a rudimentary form of molecular proofreading, would have evolved in the generations between the Ur-organism(s) and LUCA. Presumably, other genetic codes evolved alongside the modern one, with their own molecular proofreading mechanisms for replication as well as transcription and translation. It just happens that LUCA already possessed the modern code, which it inherited from a parent cell. Then, LUCA's progeny outcompeted to extinction all users of other genetic codes, and even all other users of the modern code.

What Theobald (2010) overwhelmingly showed was that while LUCA was not the very first cell, it was a single cell the same way the Y-Chromosomal Adam was a single man. In principle the same pattern is at work, but here it applies to all living things rather than just humans in particular. The modern universal commonalities (which by the way are more than just the Genetic Code which is a term for the translation code; they also include use of A, T, G, C, and U as opposed to hundreds of other nucleotide monomers which are chemically possible; the use of sinistral isomers of 20 amino acids, as opposed to any dextral isomers or hundreds more chemically possible amino acid monomers; the universal use of dextral isomers of sugar monomers as primary fuel to make ATP; the use of ATP as opposed to other equally unstable molecules as intermediate fuel in metabolic pathways; etc.) are exceedingly unlikely to arise from horizontal gene transfer alone. The odds of that scenario are 1 in 10³⁴⁸⁹, as the Article already notes in the Lead. As 10³⁴⁸⁹ is a mind-blowingly huge number, the logical conclusion is that a single LUCA did exist as explained above.

Horizontal transfers did take place, among LUCA's progeny, that is to say among ancient cells which already shared an even older common ancestor. This is the meaning of, exact quote, "A model with a single common ancestor but allowing for some gene swapping among species" (Emphasis added), as quoted from Saey (2010).

Now, the evolution of the code does make it difficult, though perhaps not impossible, to trace the lineage of a specific Ur-organism to LUCA. (In fact, reconstructing any Ur-organisms is far more difficult than reconstructing LUCA, for the same reasons.) That being said, it has no bearing on the existence of LUCA as a single cell whose progeny survived. The landmark paper made it clear that LUCA did exist, that it was a single cell albeit a member of a diverse community at the time, and that all except the progeny of that individual became extinct quite early in microbial evolution.

All this being explained, the earlier results in Woese (1998) are not entirely negated, with respect to Ur-organisms. However, they are compromised in the sense that, in light of the results in Theobald (2010) and Saey (2010), they apply mainly to Ur-organisms and should not be taken as arguments against the existence of a single LUCA. The Mysterious El Willstro (talk) 01:22, 28 June 2014 (UTC)