Talk:Last universal ancestor

From Wikipedia, the free encyclopedia
Jump to: navigation, search
          This article is of interest to the following WikiProjects:
WikiProject Genetics (Rated Start-class, Top-importance)
WikiProject icon This article is within the scope of WikiProject Genetics, a collaborative effort to improve the coverage of Genetics on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
Start-Class article Start  This article has been rated as Start-Class on the project's quality scale.
 Top  This article has been rated as Top-importance on the project's importance scale.
 
WikiProject Evolutionary biology (Rated Start-class, Top-importance)
WikiProject icon This article is part of WikiProject Evolutionary biology, an attempt at building a useful set of articles on evolutionary biology and its associated subfields such as population genetics, quantitative genetics, molecular evolution, phylogenetics, evolutionary developmental biology. It is distinct from the WikiProject Tree of Life in that it attempts to cover patterns, process and theory rather than systematics and taxonomy). If you would like to participate, there are some suggestions on this page (see also Wikipedia:Contributing FAQ for more information) or visit WikiProject Evolutionary biology
Start-Class article Start  This article has been rated as Start-Class on the project's quality scale.
 Top  This article has been rated as Top-importance on the project's importance scale.
 
WikiProject Human Genetic History (Rated Start-class, Mid-importance)
WikiProject icon This article is within the scope of WikiProject Human Genetic History, a collaborative effort to improve the coverage of genetic genealogy, population genetics, and associated theory and methods articles on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
Start-Class article Start  This article has been rated as Start-Class on the quality scale.
 Mid  This article has been rated as Mid-importance on the importance scale.
 
WikiProject Computational Biology (Rated C-class, Mid-importance)
WikiProject icon This article is within the scope of WikiProject Computational Biology, a collaborative effort to improve the coverage of Computational Biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
C-Class article C  This article has been rated as C-Class on the quality scale.
 Mid  This article has been rated as Mid-importance on the importance scale.
 
WikiProject Biology (Rated B-class, Top-importance)
WikiProject icon Last universal ancestor is part of the WikiProject Biology, an effort to build a comprehensive and detailed guide to biology on Wikipedia.
Leave messages on the WikiProject talk page.
B-Class article B  This article has been rated as B-Class on the project's quality scale.
 Top  This article has been rated as Top-importance on the project's importance scale.
 

Features Section[edit]

I removed two points from the features section. If people have objections to this, let's discuss it here :)

  • All other properties of the organism were the result of protein functions.
This seems to me to be a fairly vague statement, which leaves it very open to interpretation by the reader. What does it mean by "all other" properties? Even given this ambiguity, I find it very hard to imagine how this could be true in any interpretation. Many properties of organisms depend, for instance, on the lipids in their membranes, something which certainly true for LUCA as well. Also, this statement disregards the importance of catalytic or otherwise functional RNAs, which were probably even more prominent in LUCA than in most modern organisms (where they are still very significant!) given that most of the original catalytic functions of the life were probably carried out by RNAs and later replaced by proteins. Anyways, I find this point uninformative at best and downright misleading at worst.
  • Glucose could be used as a source of energy and carbon; only the D-isomer was used.
My problem here is not with the D-isomer, but rather with the assertion that LUCA metabolized glucose. While this is certainly possible, given the immense variety of metabolisms present in modern bacteria (which are discussed in the PNAS article currently cited as ref 8), LUCA's metabolism (or range of metabolisms) is likely not known with much certainty. Unless someone can find some sources suggesting that LUCA metabolized glucose, I think this statement is quite unfounded. A2soup (talk) 01:36, 4 May 2013 (UTC)

'All organisms', period?[edit]

seems like this isn't the place to argue that every organism in existence is on earth right now. we shouldn't use "all currently living organisms" to refer to the descendants of the LUA unless we're also going to say that there aren't any currently living organisms unrelated to life on earth. —The preceding unsigned comment was added by 69.181.232.197 (talk) 08:23, August 23, 2007 (UTC)

Along those same lines, perhaps drop the "living" as in the LUA being the "latest living organism?" Tom Schmal 15:35, 31 October 2007 (UTC)

To those who are mentioning Extra-Terrestrials[edit]

Other biospheres would presumably have their own respective LUCAs and LUCA heritages, and since we live in a very young universe that is still mostly hydrogen with which to fuel future stars, a much newer biosphere even in the same universe (as opposed to a parallel one) might be developing in the LUCA phase of its evolution right now. The Mysterious El Willstro (talk) 22:08, 12 October 2010 (UTC)

Last or First?[edit]

If this is the "Last" common ancestor, what was the First one? Tom Schmal 13:00, 24 July 2007 (UTC)

The first sentence seems to be clear in that direction to me. First common ancestor is something really hypothetical (and a bit creationist, if you ask me). To put it simple, consider the LUCA as part of a wider group of people. He is the great-great-...-grandfather of everyone alive today, while none of the other people have any living descendants. » byeee 07:56, 27 July 2007 (UTC)

How many "universal" ancestors could there be? Wouldn't it be more correct if this ancestor were named the "First Common Ancestor?" So as between humans and chimps, for example, this would be the First Common Ancestor, then there would be millions of other common ancestors until finally five million years ago we would come to the Last Common Ancestor where the two species go their different ways.

Or maybe just the "Universal Ancestor." The "Last" seems redundant at best. Tom Schmal 15:06, 31 July 2007 (UTC)

If I don't reflect on it a whole bunch, it seems right. But if I start thinking whether Last or First is best, my head goes spinning. But, as you said the difference between the First and Last yourself, the Last seems much more important - and the scope of this article. » byeee 17:44, 31 July 2007 (UTC)
It's definitely last. There may have been earlier common ancestors, who may have had several descendant branches, but only one of these descendants is both LAST and COMMON. Draw a tree if you don't see it right away. Piet | Talk 20:31, 15 January 2008 (UTC)
I thought I'd add my two cents as I've referenced this section of talk below. As I see it there are three significant individual organisms related to the origins of life on Earth.
  1. First Living Organism (FLO) - This is the first instance of life arising on Earth. It is not necessarily an ancestor of any life currently living as its entire line may have died out after another line (that line leading to all current life) independently came into existence.
  2. First Universal Ancestor (FUA) - This is the first organism in the line leading to all life on Earth today. This organism would have no ancestors and would have arisen abiogenically as had the FLO above. The FUA would be the oldest ancestor of the LUA.
  3. Last Universal Ancestor (LUA) - This is the organism that serves as common ancestor to all life today. It represents the only surviving branch of the FUA's line. The FUA's line may have had several other branches (none of which were ancestral to all current life) that have died out leaving only the LUA's descendents.
Hopefully that's fairly clear. I think it illustrates the difference between the Last Universal Ancestor and the First Universal Ancestor and explains why this article is called what it is.
Note: I think from what I'm seeing online that another name for the FUA is the Ur-organism (Emmanuelm explains below that this means original organism).
-Thibbs (talk) 17:49, 5 May 2008 (UTC)
(outdent) Unfortunately it seems that the subtleties of these concepts have proven more elusive than my basic explanations could compete with. To clarify the topic I will describe the terms FLO, FUA, and LUA in terms of the theoretical organisms given to us by Darwin in his Tree of Life (Note: although this link is accurate I would recommend finding a clearer copy to refer to the details).
edit: a clearer copy Thibbs (talk) 17:03, 6 May 2008 (UTC)
  • Referring once more to the definitions for FLO, FUA, and LUA provided above, let us begin by imagining that the LUA is represented by organism a3 from Darwin's chart (let us extend the d-line to the 14th generation to represent bacteria, the f-line represent archaea, and the a5-a6-line represent eukaryota). If we now imagine that the m-line had ended at m8 and we ignore the F-, w-, and z-lines, then we can see that all living organisms at the current date (the 14th generation) descend from a3 (the LUA) and its ancestors.
  • This then allows us to view A at the 0th generation (or more properly the common ancestor of A, B, C, and D at the -1st generation) as the FUA.
  • The FLO is harder to illustrate. Let us begin by taking the same assumptions as we have for the LUA and the FLO. We now imagine that the common ancestor of A, B, C, and D is called α, the ancestor of E is ε, and the ancestor of F is φ. Let us for the moment ignore G, H, I, K, and L. Let us further imagine separate moments of abiogenesis for α, ε, and φ such that the order of their abiogenic development was first φ, second ε, and third α. The FLO, then, would be φ.
This covers the three most important players in the origin of life on earth (if we are to remain in the strictly scientific realm). It should be noted that a different table could be produced in which any two or all of the FLO, FUA, and LUA are the same organism.
  • As a final note, and to explain my mysterious dismissal of G, H, I, K, and L (from Darwin's chart), I have recently considered that there is potentially one other interesting individual who could be discussed in the topic of the origin of life. The First Living Organism in the Universe (FLOU) could be described if we imagine G, H, I, K, and L on another planet. If their common ancestor is called γ and γ is contemporaneous with φ (Earth's FLO) in the same -1st generation, then we see that φ can remain as Earth's FLO despite the existence of other organisms (i.e. γ) in the same generation. If we now claim that the γ-line began much earlier we can postulate that if γ's ancestor, א (the only -2nd generation-member), was the first example of life in the universe/multiverse/reality of everything then א is the FLOU.
I hope this un-muddies the water a bit. -Thibbs (talk) 16:54, 6 May 2008 (UTC)

Source?[edit]

Does anyone have a citation for the claim that LUCA lived around 3.5 billion years ago? I'd like to use it for History of Earth. — Knowledge Seeker 00:07, 29 March 2006 (UTC)


"The Last Universal Ancestor hypothesis has since been refuted on many grounds[citation needed]. For example, it was once thought that the genetic code was universal (see: universal genetic code). Back in the early 1970s, evolutionary biologists thought that a given piece of DNA specified the same protein subunit in every living thing, and that the genetic code was thus universal. Since this is something unlikely happen by chance, it was interpreted as evidence that every organism had inherited its genetic code from a single common ancestor, aka. the "Last Universal Ancestor." In 1979, however, exceptions to the code were found in mitochondria, the tiny energy factories inside cells. Biologists subsequently found exceptions in bacteria and in the nuclei of algae and single-celled animals. It is now clear that the genetic code is not the same in all living things, and that it does not provide powerful evidence that all living things evolved on a single tree of life[citation needed]. Further support that there is no "Last Universal Ancestor" has been provided over the years by lateral gene transfer in both prokaryote and eukaryote single cell organisms. This is why phylogenetic trees cannot be rooted, why almost all phylogenetic trees have different branching structures, particularly near the base of the tree, and why many organisms have been found with codons and sections of their DNA sequence that are unrelated to any other species[citation needed]."

- I am very suspicious of this paragraph. It has no sources cited, and it does not match up at all with what I was taught in multiple University level Biology classes (Including Cellular, and Microbiology). I was taught that all known exceptions to the universality of the genetic code were believed to be acquired characteristics. Most of them are also attributable to post translational modification as well (such as the presence of Selenocysteine in mammals.Cadallin 20:50, 1 April 2007 (UTC)Cadallin

I have a page "Last Common Ancestor" so I put in a link to it, but no trail, so I will sign it here. Also whoever put in the text above about the refutation also put it in Last Common Ancestor reference section where I really don't think it belongs. Tom Schmal 22:54, 9 April 2007 (UTC)

Religious Bias[edit]

There is no "Criticism" Section currently in the Article to discuss. (If such a Section is created in the future, just make a new Talk Page Section about it.) The Mysterious El Willstro (talk) 18:20, 16 May 2013 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

The information in the "Criticism" section can be broadly defined as "Creation Science." These are arguments commonly used to support the pre-conceived conclusion that humans evolved independently of all other organisms on earth. Basically, the author's position is that instead of there being ONE family tree for all life on earth, there are a bunch of different trees and that in some cases(particularly that of humans) the tree is simply linear. While the article should probably contain some general comment to the effect that there are some other non-trivial hypotheses about the exact path to our current biodiversity, it is NOT acceptable for non-NPOV theories outside sphere of accepted science to comrprise 60+% of the article. —The preceding unsigned comment was added by 167.83.10.20 (talk) 20:15, 11 April 2007 (UTC).

Let us PLEASE not get religious "criticisms" into this article. That should belong in Conservapedia. Let's keep it proper science on this page. — Preceding unsigned comment added by 149.172.153.15 (talk) 10:29, 22 November 2012 (UTC)

I am removing the "LUCA is refuted" paragraph, it's thinly disguised creationism. The somewhat relevant parts of it, about problems rooting the tree of life, are already addressed in the article via the section on gene transfer.

-Blueshifter 15:26, 29 April 2007 (UTC)

The criticism section smacks of creationist nonsense right from the first sentance. —Preceding unsigned comment added by 12.33.211.29 (talkcontribs) 09:56, 20 June 2007

It shouldn't automatically be dismissed as 'nonsense'. People need to be open to other viewpoints and interpretations of the scientific evidence. I do understand the rules of needing reliable/verified material for the wiki, though. But people still need to have more respect for other viewpoints. — Preceding unsigned comment added by 98.213.92.109 (talkcontribs) 05:06, 9 January 2012

Removed unsourced, weasely criticism section. There is no doubt some published scientific criticism - so find and cite it if the section is to be re-written. Vsmith 11:28, 20 June 2007 (UTC)


The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

"What we know" section created[edit]

No such Section exists, same as the above thread. The Mysterious El Willstro (talk) 18:21, 16 May 2013 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

I created a paragraph that attempts to list all the properties shared by all independently living organisms (not viruses), based on the assumption that the LUA must also have had these properties. I had lots of fun doing this. It is clearly incomplete; be bold, improve it. Emmanuelm (talk) 16:15, 11 January 2008 (UTC)

It's very interesting, nice work. It would be better if you had a source, but I won't touch it. One thing struck me however: "almost all independently living organisms". Considering the scope of the LUA concept, "almost" has no place there. I've removed it, at the risk of being less exact(?) In this place however "almost" is a weasel word. But again, nice work. Piet | Talk 20:37, 15 January 2008 (UTC)
Thanks Piet. I added two references only; they were surprisingly difficult to find. Please help by finding more. Emmanuelm (talk) 17:00, 18 January 2008 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

"Darwin's black box and the LUA" section created[edit]

Ditto. The Mysterious El Willstro (talk) 18:21, 16 May 2013 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

I added this paragraph. A bit weak, but I think it is interesting. If you delete it, I will not revert. Emmanuelm (talk) 17:08, 11 January 2008 (UTC)


The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Microtubule-based locomotion?[edit]

What source - or for that matter, what line of reasoning - advocates microtubule-based locomotion in the last universal ancestor, as currently purported by this article? MicroProf (talk) 02:46, 27 February 2008 (UTC)

I guess you are right; the line is removed. Emmanuelm (talk) 00:47, 16 March 2008 (UTC)

Merger proposal[edit]

The Ur-organism Article specifies that the Ur-organism is even earlier, the ancestor of LUCA. Besides, this Section has been inactive for years. There can't be any harm in closing it now. The Mysterious El Willstro (talk) 18:26, 16 May 2013 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

According to the definition of Ur-organism found in its article, there seems to be no need for both articles on "ur-organism" and "LUCA". I am not familiar with the ur-organism concept, but it also seems possible to me that it actually refers to the first instance of life or even the First Common Ancestor (as discussed above), and that the definition listed at Ur-organism is incorrect. Does anyone know anything more about this? Should the two be merged and disambiguation be set up or should the definition of ur-organism simply be rewritten accurately? -Thibbs (talk) 21:58, 3 May 2008 (UTC)

In Google scholar, a search for "ur-organism" returned 8 hits, only one article using this term in its title. A search for "last universal common ancestor" return 53,000 hits. As per WP:Fringe, I vote we kill the Ur-organism article and redirect it to this one. Emmanuelm (talk) 20:18, 4 May 2008 (UTC)
Sounds good to me unless as I suggested earlier ur-organism actually means something different than it purports to in the ur-organism article. I'll try to do a little follow up on this. -Thibbs (talk) 23:36, 4 May 2008 (UTC)
OK, well this is proving to be more of a challenge than I'd thought. There seems to be much confusion of language online about what the term means. Harold J. Morowitz' book, Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis (1993, Yale University Press) suggests that

"We envision the Ur-cells as being very simple, whereas the universal ancestor must—by comparison to these—have been quite complex. Thus, the gap between the approach from above and the approach from below must be filled by an evolutionary path from the ur-organism to the universal ancestor. The problem is not simply the origin of life, it is the physical formation of the the Ur-organism and a subsequent evolutionary epoch giving rise to the universal ancestor."

Later in the chapter he refers to the ur-organism as "a protobiotic form." This source, then, clearly supports the idea that "ur-organism" is a term for the First Universal Ancestor (not to be confused with the First Living Organism) rather than the Last Universal Ancestor. There are a few corroboratory sources from the social sciences or religious scholarship which I would hesitate to rely upon (eg. Rist's paper and Unger's article which was referenced in Google Scholar...). There are also an irritating number of folks online who employ the term "ur organism" to mean "your organism" as in "u take ur organism and put it undr teh microscope." The wiki article, Ur-organism, references Darwin as the originator of the term and I have run text searches on online versions of Origin of Species to no avail. I have not yet run tests on Descent of Man or his other works. I notice that Oparin has also been referenced but I have not yet examined his use of the term (if indeed he has used it at all). Before doing difficult-to-reverse changes to wiki, though, it seems to me that we need more authority than the unreferenced definition found in the ur-organism article. If anyone can find any information on the use of this term it would be very helpful. -Thibbs (talk) 00:37, 5 May 2008 (UTC)
Another option, incidentally, is to simply merge "ur-organism" with "abiogenesis" somehow. Prior to any merge, though, we need to get consensus on the definition of the term "ur-organism." -Thibbs (talk) 00:41, 5 May 2008 (UTC)
Another search at Google Books found two mentions in the context of evolution. No Darwin, no Oparin. Fringe comes to mind once more.
BTW, I'll bet (less than a dollar) that this weird word comes from Ur, the birth city of Abraham, the founder of all monotheistic religions. Emmanuelm (talk) 03:23, 5 May 2008 (UTC)
I lost my cheap bet with myself. From Audi Quattro the "Ur-" prefix is a German augmentative used, in this case, to mean "original" . Emmanuelm (talk) 03:30, 5 May 2008 (UTC)
Wow, Thibbs, the LUCA concept is a theoretical construct based on analogy (genetic and others) between currently living organisms. The adjective "last" is used to mean "most recent". It refers to the fact that this bug was most certainly not the first living organism but was itself the result of a long evolution. This evolution is, unfortunately, locked in a blackbox that may never be cracked by science. This is briefly explained in the article. You may expand it if you have time. Emmanuelm (talk) 13:53, 6 May 2008 (UTC)
Emmanuelm, you are incorrect that the term LUCA requires that "this bug was most certainly not the first living organism but was itself the result of a long evolution." It is possible that LUCA could be the same as the first instance of life in the universe, although this is more unlikely than your guess. I am very cognizant of the fact that this article is about the "last" (meaning "most recent") ancestor common to all life and I don't believe I've made any claims to the contrary. You must recognize, however, that there is a small chance that the last common ancestor to all current life is also the last common ancestor to all life that ever lived. I don't propose here to change the article to focus on this, but I certainly object to the assertion that this LUCA "bug" was most certainly not the first living organism when in fact it may well have been. (Incidentally I would also caution against using the term "bug" to describe the LUCA as bugs are, in fact, orders of magnitude more complex than the LUCA organism would statistically certainly have been). Perhaps to clarify I should mention that the FUA discussed above would also be a theoretical concept based on genetic analogy between organisms, however the scope of its analogical pool would include organisms (non-extant) that are not included in the line of the LUCA's ancestry. I will add a quick example to better explain this tricky concept above.
I think we have drifted away from the main topic of this thread, however. My question, to reiterate, was: Does the term "ur-organism" mean "LUCA," "First Universal Ancestor," or "First Living Organism?"
PS - Thanks for your contributions so far, Emmanuelm. I am glad at least someone else is aware of this corner of wiki. If there is anyone else out there who knows anything about the issue at hand or can help in any way please feel free to chime in. -Thibbs (talk) 15:52, 6 May 2008 (UTC)
Once this merge dispute is resolved, can someone fix cenancestor to point to the best article describing it? Thanks. StevePrutz (talk) 04:37, 22 May 2008 (UTC)
After a quick Google, I conclude that cenancestor is a synonym of LUCA. I changed the redirection of cenancestor to reflect this. I still think that ur-organism is different and should probably be redirected to origin of life. Emmanuelm (talk) 21:22, 23 May 2008 (UTC)
I agree with Emmanuelm that ur-organism is most likely different from LUCA. I had written to the creator of the article on "ur-organism" and he has not responded. I will go ahead and remove the redirect tags for ur-organism->LUCA and rewrite the lead for ur-organism so that it can no longer be confused with the LUCA. -Thibbs (talk) 21:36, 24 May 2008 (UTC)
Thibbs, I like what you wrote in Ur-organism; I clarified it further. I think that article can now be laid to sleep.
Now, to come back to a much more interesting argument, you wrote above I certainly object to the assertion that this LUCA "bug" was most certainly not the first living organism when in fact it may well have been. Please have a look at some very cool animated videos of DNA duplication, transcription and RNA translation linked here. Then tell me again: do you honestly believe that this extraordinarily complex and precise machinery which, by the way, was fully functional in the LUA, could be the first functioning cell? When the chance of an event occurring is vanishingly low, one can say it "most certainly" did not happen this way.
I let good sense dictate my writing, not absurd rhetoric. Good sense tells me that such a complex process is the result of a very long evolution. The fact that we have no trace of this evolution is unfortunate but does not make it non-existent. Emmanuelm (talk) 15:05, 29 May 2008 (UTC)
Thank you. I agree that "ur-organism" is more or less finished now and I think your additions were valuable there. A few unsourced claims remain such as the Darwin connection, but I think that on the whole it is much less confusing now.
As far as my earlier suggestion that there was a small chance that the hypothetical LUA may have been the first living organism, I should start by clarifying that I don't consider this scenario likely. I tried somewhat unsuccessfully to make this clear in the sentences just prior to the one you've quoted. Regarless of my doubts as to its likelihood, however, it is important to remember that strict adherence to the definition of LUA should not be confused with "absurd rhetoric" considering that even an organism which has left no trace may still be described accurately. With nothing but a definition and the analogies that can be drawn from extant organisms, it strikes me as rather foolhardy to make statistical certifications of the processes by which the LUA's hereditary information was replicated when the scientific community is simultanously statistically certain that most extant organisms remain undiscovered. All it would take would be the discovery of an RNA-based lifeform to chip away at the currently "known" attributes of this conceptual LUA organism. I believe such a discovery is unlikely but hardly "vanishingly low"... In general I believe that when speaking of the LUA we must guard ourselves against fixing on any of these "known" attributes as "most certainly" true even if we strongly believe them to be so based on current evidence.
Please also note that I am not proposing to change the text of the article to reflect this hypothetical scenario involving the discovery of an RNA-based lifeform. I believe that such a suggestion might unnecessarily muddy the waters. Yet I maintain that it was quite pertinent to bring up the possibility that the LUA and first living organism could be one and the same insofar as this suggestion arose during a dialogue about hypothetical organisms restricted to only the talk page.
PS - That was a pretty cool animated video. It's a pity about the video quality, but I certainly agree with your argument that such complexity could not have come from a single evolutionary step short of some sort of non-evolutionary act such as interstellar seeding, etc. I am actually quite a sucker for animated demonstrations of biological concepts, so my thanks to you. -Thibbs (talk) 22:22, 29 May 2008 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Misconceptions[edit]

This section needs to be expanded, or better yet scrapped completely with the information being redistributed throughout the article. Phoenix1304 (talk) 08:35, 28 May 2008 (UTC)

Phoenix, be bold, do it. Emmanuelm (talk) 12:54, 28 May 2008 (UTC)

New Scientist Article 21. JAN 2009[edit]

This looks interesting. Info from this source might be good to extend the article with.

"Why Darwin was wrong about the tree of life". New Scientist (2692): 34–39. 21 January 2009. 

--InsufficientData (talk) 21:47, 25 January 2009 (UTC)

That was before the big statistical test in 2010. We have new evidence in favor of LUCA since that article was written. The Mysterious El Willstro (talk) 18:29, 16 May 2013 (UTC)

Problems with Some "Evidence"[edit]

This needs to be updated with respect to some of the evidence points given in the "Evidence of universal common descent". There are elements of this that, while evidentiary, is not true of all current life on earth.

Examples include:

  • Re the repeated statement that "only 20 amino acids are used": Human DNA codes for 22 amino acids (though, admittedly, only 20 of those are directly coded by the codons) and those 22 acids can all be used in proteins. It might be better to say that the same common 20 amino acids are used, rather than "only".
  • DNA is, indeed, always composed of four nucleotides, but some forms of life substitute one of the nucleotides for a different one. That is, not all life uses the combination "(deoxyadenosine, deoxycytidine, deoxythymidine and deoxyguanosine)"; some life uses a DNA in which one of these is replaced by some other deoxynucleotide.
  • I would have to dig for this, but I think I read that not all life uses the glycolysis pathway. Some of the archaea H2S, if I remember correctly, do not implement this pathway.

There is plenty of evidence still, of the last universal ancestor; this is just a matter of correcting the article qualifications to be more accurate in view of later discoveries.

CoyneT talk
Good points. Please don't be shy about editing, though. If you see something that needs to be corrected, be bold. -Thibbs (talk) 19:35, 29 May 2010 (UTC)
CoyneT, let's see a source regarding your claim of human DNA coding for synthases to make non-LUCA amino acids. (They must be directly encoded by the codons to be "coded for" in the DNA, otherwise a synthase enzyme for the amino acid in question would have to be encoded.) I'm well aware that plants make extra amino acids as a defense mechanism, but I'm not so sure we make amino acids outside the main 20. The Mysterious El Willstro (talk) 03:37, 25 March 2012 (UTC)

"Probabilities"[edit]

I don't have access to the cited Science News article, but numbers as large as 10^2860 are ridiculous. This must be a typo. Mphelbert (talk) 18:27, 24 July 2010 (UTC)

I'd have thought so, but I have access to the article through my university and it does indeed say "Therefore, UCA is at least 10^(2,860) times more probable than the closest competing hypothesis." Quite an incredible number, but it's what's in the paper.


These numbers are correct. There are many places in Statistical Mechanics, Quantum Mechanics, and other "hard" sciences where such probabilities show up. These numbers are from a paper in Nature, which is arguably the most prestigious science journal in the world and they are correct. 138.253.48.109 (talk) 11:37, 23 August 2010 (UTC) Steel, David; Penny (13 May 2010). "Origins of life: Common ancestry put to the test" 465 (7295). London: Macmillan Publishers Limited. pp. 168–169. doi:10.1038/465168a. ISSN 0028-0836.  Unknown parameter |Journal= ignored (|journal= suggested) (help); More than one of |first1= and |first= specified (help)

Theobald, Douglas L. (13 May 2010). "A formal test of the theory of universal common ancestry". Nature (London: Macmillan Publishers Limited) 465 (7295): 219–222. doi:10.1038/nature09014. ISSN 0028-0836.  I do not know why the two Nature citations were removed, but I put them in originally, and have restored them.

Nick Beeson (talk) 11:39, 6 April 2011 (UTC)

Falsified material in this article.[edit]

Concerning this abstract/paper by Douglas L. Theobald (Theobald DL on his paper) which is cited in the Wikipedia article at http://en.wikipedia.org/wiki/Universal_ancestor


> "Nature. 2010 May 13; 465(7295):219-22. > A formal test of the theory of universal common ancestry. > Theobald DL. > Department of Biochemistry, Brandeis University, Waltham, > Massachusetts 01778, USA. dtheob...@brandeis.edu > Comment in: > * Nature. 2010 May 13;465(7295):168-9. > Abstract > Universal common ancestry (UCA) is a central pillar of modern > evolutionary theory. As first suggested by Darwin, the theory of UCA > posits that all extant terrestrial organisms share a common genetic > heritage, each being the genealogical descendant of a single species > from the distant past. ***The classic evidence for UCA, although > massive, is largely restricted to 'local' common ancestry-for example, > of specific phyla rather than the entirety of life-and has yet to > fully integrate the recent advances from modern phylogenetics and > probability theory. Although UCA is widely assumed, it has rarely been > subjected to formal quantitative testing,*** and this has led to > critical commentary emphasizing the intrinsic technical difficulties > in empirically evaluating a theory of such broad scope. Furthermore, > several researchers have proposed that early life was characterized by > rampant horizontal gene transfer, ****leading some to question the > monophyly of life.**** Here I provide the FIRST, to my knowledge, > formal, fundamental test of UCA, without assuming that sequence > similarity implies genetic kinship. I test UCA by applying model > selection theory to molecular phylogenies, focusing on a set of > ubiquitously conserved proteins that are proposed to be orthologous. > Among a wide range of biological models involving the independent > ancestry of major taxonomic groups, the model selection tests are > found to overwhelmingly support UCA irrespective of the presence of > horizontal gene transfer and symbiotic fusion events. These results > provide powerful statistical evidence corroborating the monophyly of > all known life. > PMID: 20463738 [PubMed - indexed for MEDLINE]"

> From - http://www.ncbi.nlm.nih.gov/pubmed/20463738 (fromhttp://en.wikipedia.org/wiki/Evolution)


Look how in the following that two Wikipedia contributors (Mike Steel and David Penny) have falsified data from the SAME paper/abstract (abstract by Theobald, DL, also known as Douglas L. Theobald) that I cited above, crediting *themselves* with writing a book or something or other (likely a letter to the magazine that printed Theobald's paper) on the subject of the article/paper on the SAME DATE as the article/paper and linking to Theobald's paper.

From Wikipedia's article Last Common Ancestor at - http://en.wikipedia.org/wiki/Universal_ancestor - last updated 17 Sept. 2010

David Penny and Mike Steel write (notice the quoted material is a partial sentence only and IS NOT CONTAINED in the abstract/paper by Theobald, which is at the top of this post): "There is strong quantitative support, by a formal test"[1] for the theory that all living organisms on Earth are descended from a common ancestor.[4]"

Note who their sources for this statement are: themselves (#4), and the paper/abstract I cited above (#1). And the PMID numbers in both #1 and #4 are links which lead to the same abstract/paper by Theobald.

  1. 1. ^ a b c d Theobald, Douglas L. (13 May 2010). "A formal test of

the theory of universal common ancestry". Nature 465 (7295): 219–222. doi:10.1038/nature09014. PMID 20463738.

  1. 4. ^ a b Steel, Mike; Penny, David (13 May 2010). "Origins of life:

Common ancestry put to the test". Nature 465 (7295): 168–169. doi: 10.1038/465168a. PMID 2046372

Linda 444 (talk) 19:07, 27 September 2010 (UTC)


Linda 444,

I am sorry that you find this suspicious, but there is nothing the least suspicious about this.
It is common in the two most prestigious scientific journals in the world: Nature, and Science. They both have a "commentary" section where the publish "editorials" explaining articles published later in the same issue. The goal of editorials is to:
  • inform the educated layman why an article is important;
  • show how it fits into the research goals of a field; and
  • discuss its impact on other fields.
These editorials always cite the article in the same issue of the journal, and often cite the editorial author's own research. The reader is expected to trust the journal editor to have chosen an expert in the field. who will present a neutral point of view. The readers know the author's work is impacted by the article under discussion, and that they will therefore cite their own work.
I cited the commentary precisely because it tells the audience why the research is important in words Wikipedia readers can be expected to understand.
Nick Beeson (talk) 12:56, 6 April 2011 (UTC)

Species or single cell?[edit]

Are we talking about a species here, or about a single, individual cell? -- 77.7.152.59 (talk) 02:03, 24 November 2010 (UTC)

We are talking about 1 individual globule (early cell) whose lineage survived beyond the very earliest evolutionary period. There were any number of globules of the molecules now known as biological polymers that came together during the Primordial Soup Event, but only 1 whose lineage survived, and the evidence for this lies in the biosphere's common chemical features some of which are already listed in the Article. Does that make sense? The Mysterious El Willstro (talk) 07:01, 7 February 2011 (UTC)
I suppose we can be fairly certain this was a single cell organism. The single cell status is referred to in the last few bullet points, but not stated explicitly. It probably also had a cell wall as this is primitive to both Archeans and Eubacteria. Why aren't these rather basic traits mentioned in the article? I am sure the reader not well versed in cell biology would like some "what was this critter like" type of gross morphology information, not just the technicalities of the internal workings. Petter Bøckman (talk) 22:32, 28 December 2011 (UTC)
Petter Bøckman, in principle I agree. The issue is that many finer details of what this critter was like are actually not conclusively known. The Mysterious El Willstro (talk) 03:42, 25 March 2012 (UTC)
Actually, the finer details of this critter are surprisingly well known (details of metabolism etc.). What I’m after are the larger traits which it seems the authors of this article have not bothered with as they are self-evident to anyone with a smattering of biology (single cell, cell wall, generally “bacteria-like”). I was thinking a sentence like:
"Considering what we know of the offspring groups (see phylogenetic bracketing), the LUCA was a small, single-cell organism. It would have had a cell wall and a ring-shaped coil of DNA (or possibly RNA[1]) floating freely within the cell, like modern bacteria. It would likely not have stood out against a collection of modern generalized small size bacteria." Petter Bøckman (talk) 13:13, 30 April 2012 (UTC)
By finer details, I mean we don't know LUCA's exact genome and proteome (and unfortunately, it's quite possible that we never will). We don't know anything else at that level of detail, for that matter.
More to the point, I support your sentence to be added, minus the "(or possibly RNA)" part. Bearing in mind that this is the Last Universal Common Ancestor, not the abiogenic Ur-organism, it would have been post-RNA-world, although a very early DNA-based organism. (I talked about this with my Micro. Professor before I graduated this past May.) The Mysterious El Willstro (talk) 18:15, 17 July 2012 (UTC)
Just to dig this up again, someone explain for me, why it couldn't have been a colony of sister cells, of which some branched off into this and some into that. Or would that just mean LUCA is the first of that cell lineage? Couldn't some very similar but non-identical cells have started the various lines? Why not? I have the idea of a certain amount of little cells floating around at the time, quite advanced compared to early lipid-bags of replicating proteins, but with some genetic variation. So why would only one of them be the ancestor? Don't most animals evolve from populations of ancestor animals, rather than just the one? With a genetic range before speciation chops the range off. I'm not arguing, I want to know, but this isn't obvious from what I can read here. 94.197.121.12 (talk) 22:31, 27 May 2015 (UTC)

Arbitrary choice of codons?[edit]

This article states that there was an arbitrary choice of codon patterning. I am not an expert, but last I checked, there was evidence that each codon tends to be more attracted to its amino acid in solution than to any other. Also, to describe the universal ancestor as already having 3-base codons etc should be cited in my opinion. Any such organism must have evolved from something simpler, or been put there by an intelligent designer. - Richard Cavell (talk) 12:11, 19 March 2011 (UTC)

There were simpler globules (I say "globules" because calling them "organisms" whatsoever is rather debatable) that existed before LUCA. LUCA has "Last" in its name for partly that very reason: It lived fairly late in the Abiogenesis Event. The Mysterious El Willstro (talk) 03:48, 25 March 2012 (UTC)

Cavalier-Smith phylogeny?![edit]

I am baffled by the appearance of a phylogenitic tree based on cavalier-smith papers being presented as the accepted view of the tree of life. It is all but the accepted view. I find the Cavalier-smith papers very interesting and bold, but they must be read in context (the reviewers' comments on his biology direct paper spell it out). Molecular phylogeny may be wrong, but until the consensus is against it, it should be the main view presented. Putting together a cladogram requires a lot of effort and I do not want to summarily delete it, but in most scientific litterature LUCA is not a bacterium, but a bacterium/neomuran ancestor. Most papers that do claim it to be a bacterium place it in the Firmicutes and not with a basal phylum "Chloroflexi" (the phylum does not have a proper name and Cavalier-Smith coined the term Chlorobacteria, but that is not how the system works another example why the papers require a pinch of salt). Therefore should this large tree be transfered elsewhere? --Squidonius (talk) 03:49, 1 August 2011 (UTC) Moved here for now: Phylogeny[2][3]

This page is about phylogeny based on a controversial theory. For other phylogenies, see bacterial phyla.
  LUCA

?Armatimonadetes (Candidate division OP10)



Chlorobacteria1,2,3 (Green Non-sulfur or anoygenic photoheterotrophic Eubacteria)




Deinococci1,2,3


  Glycobacteria

Cyanobacteria2,3 (Blue-green Algae/Bacteria)



  Gracilicutes3

Spirochaetes (Spiral-shaped Eubacteria)



  Sphingobacteria

Gemmatimonas aurantiaca (DAP-less cell wall Eubacteria)



Fibrobacter




Chlorobi (Green Sulfur Eubacteria)



Bacteroidetes




  Exoflagellata
  Planctobacteria

?'Candidatus Poribacter'



Planctomycetes (Peptidoglycan-less Cell Wall Eubacteria)




Chlamydiales




Lentisphaerae (Candidate division vadinBE97)



Verrucomicrobia







?Caldisericum exile (Candidate division OP5)


  Geobacteria

Acidobacteria


  Ferrobacteria

Chrysiogenaceae



Nitrospiraceae



Deferribacteres






Thermodesulfobacteriaceae



Aquificales



Proteobacteria







  Unibacteria

?Fusobacteriales3



Thermotogales




Heliobacteriaceae


  Posibacteria
  Endobacteria

Dictyoglomus




Mollicutes (Cellwall-less Endobacteria)



Teichobacteria




  Actinobacteria

?Nostocoida limicola I



?Candidatus Planktophila limnetica



?Cathayosporangium alboflavum



?Tonsillophilus suis



Rubrobacteridae




Coriobacteriaceae




Nitriliruptoridae



Acidimicrobiales


  Proteates

?Boyliae praeputiale



?Frankia alni4,5,7



Acidothermus cellulolyticus4,5,7



Cryptosporangiaceae4



Nakamurellaceae4,5



Geodermatophilaceae4,5,7



Sporichthya4,5,6,7




Streptomyces5



Catenulisporiineae





Kineosporiaceae5,7



Micrococcineae6 [incl. Actinomycetaceae, Bifidobacteriaceae]





Streptosporangiineae5



Propionibacteriineae7



Jiangellaceae



Actinocatenispora



Micromonosporaceae7




Glycomycetaceae




Thermomonospora chromogena5



Thermobispora bispora5






Pseudonocardiineae7 [incl. Actinopolyspora]



Corynebacteriineae7 [incl. Mycobacteriales]




  Neomura

Archaeabacteria



Eukaryota (Nucleic organisms)














Notes:
1 Eobacteria
2 Glidobacteria
3 Negibacteria
4 Frankiineae
5 Streptomycetes
6 Arthrobacteria
7 Arabobacteria (Neomura stem from within Arabobacteria)
8 Archaeobacteria
Eurybacteria = Selenobacteriales, Heliobacteriaceae, Fusobacteriales & Thermotogales
Aphragmabacteria = Mollicutes & Erysilothrichia
Terrabacteria: Chlorobacteri, Deinococci, Cyanobacteria, Endobacteria, Actinobacteria & ?Fusobacteria
Selabacteria: Terrabacteria & Hydrobacteria

♠ Strain found at the National Center for Biotechnology Information (NCBI) but has no standing with the Bacteriological Code (1990 and subsequent Revision) as detailed by List of Prokaryotic names with Standing in Nomenclature (LPSN) as a result of the following reasons:
• No pure culture isolated or available for Prokayotes.
• Not validly published because the effective publication only documents deposit of the type strain in a single recognized culture collection.
• Not approved and published by the International Journal of Systematic Biology or the International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM).

That looks like it has enough sources to discuss it in the Article, although other possible phylogenies should be discussed as well. The Mysterious El Willstro (talk) 01:19, 30 April 2012 (UTC)

Auto-Archive[edit]

Let's start Auto-Archiving this Talk Page. The Mysterious El Willstro (talk) 01:45, 30 April 2012 (UTC)

Exceptions to the rules[edit]

My 2 cents: To my knowledge, yes, the D-epimer of glucose is used ubiquitously, but not unanimously, by life on Earth. I'm just mentioning this not to disprove the validity of the theory but for the article to carry a certain discipline that does not take liberties with scientific fact. Similarly, while L-amino acids are used almost everywhere, I believe that there are examples of D-amino acids out there as well. As with ATP: even humans use GTP, etc and other forms. It's not so much the A in ATP that gives energy --it's the energy stored in the pyrophospate bond that allows ATP --> ADP --> AMP to release energy.

Example: Burkholderia caryophylli uses L-glucose Cone snails use D-amino acids Google it if you want references.

I'm just trying to say that we can't make universal claims when they are not in fact true. You can choose to glaze over these 'details', but ultimately the absolute statements contained in the article are false. — Preceding unsigned comment added by 190.97.118.2 (talk) 03:55, 24 July 2012 (UTC)

Please click "edit" and go for it (add a source or two in brackets and someone will format them properly). Johnuniq (talk) 07:01, 24 July 2012 (UTC)
No, the general features of LUCA in the article are correct, but afterwards the descendants diversified their metabolisms and some rare exceptions appeared. For instance, conus snails use D-amino acids (a post-translational modification) but this is not an original (primitive) feature. LUCA probably used L-amino acids. The same for the other examples.--Miguelferig (talk) 21:18, 2 November 2012 (UTC)

So...[edit]

All-of-us-are-related? — Preceding unsigned comment added by 174.108.97.70 (talk) 07:22, 12 August 2012 (UTC)

Yep. Even you and me. HiLo48 (talk) 07:28, 12 August 2012 (UTC)

'Features' section[edit]

"However, the formal test was ambiguous with respect to the community of organisms hypothesis"[edit]

I respectfully think that the Wikipedia Community has misunderstood what the Biological Community has published. It's a minor misunderstanding, perhaps, but still a misunderstanding.

First of all, let's refer to every separate incident where organic molecules initially came together to form a cell-like structure as an "abiogenesis event." However many abiogenesis events there may have been, it's fairly safe to say that most of them quickly became extinct and contributed nothing whatsoever to the modern biosphere. However, let's say the lineages (progeny) of up to a dozen separate abiogenesis events survived beyond the Late Eoarchean into the Early Paleoarchean.

The thing to keep in mind is that there are myriad other chemically possible nucleotides besides the A, T (DNA only), G, C, and U (RNA only) monomenrs found in modern DNA and RNA, and for that matter there are myriad possible amino acids besides the standard 20 found in modern proteins. So, a microbe descendent from some other now-extinct abiogenesis event would most likely not even use the AT/GC rule or the same 20 amino acids that modern organisms do. As a result, microbes descendent from separate abiogenesis events would garble each other's genes and proteins and make them useless. (This would convert transferred genes into noncoding DNA, essentially erasing them as usable, expressable genes.) Thus, if 2 ancient bacterial cells were able to partake in horizontal gene transfer and actually use each other's genes to express proteins, it would imply that they had already shared an even older common ancestor at some point.

That being explained, the formal test favors a single LUCA over, for example, separate abiogenesis events being compatible by chance (very unlikely). Contrary to what the Article implies when it says the test was ambiguous regarding an early microbial community, I don't think anyone in relevant fields doubts that an early microbial community existed. At some point, though, there was an individual cell within that community, and while that cell was never alone, its descendants and only its descendents would survive beyond the Paleoarchean Era. That cell was a member of an early microbial community within which it struggled for survival, but it alone was LUCA in that its descendants survived. (Afterwards, there would be no shortage of horizontal transfer among LUCA's descendants.)

Quick side note: LUCA would have been an early DNA cell, just shortly post-RNA world. As far as the earlier explanation on horizontal transfer, though, it applies to the A, U, G, and C in RNA just as easily as the A, T, G, and C in DNA.

My suggestion for the Article: Let's make it clear that LUCA was a member of the early microbial community, and that while it was never alone it was the one from its time whose descendants survived. Suggesting that there's any doubt about the existence of an early microbial community, or that of LUCA, or that the 2 are mutually exclusive competing hypotheses, is rather misleading. The Mysterious El Willstro (talk) 19:32, 16 May 2013 (UTC)

Quite.Petter Bøckman (talk) 22:27, 16 May 2013 (UTC)

All right, folks[edit]

With Petter Bøckman's clear approval, and based on everything I've learned earning a B.S. in Biology, I have changed Passage A to Passage B in the Article.

Passage A:

"However, the formal test was ambiguous with respect to the community of organisms hypothesis, since it did not require that the last universal common ancestor be a single organism, but allowed it to be a population of organisms with different genotypes that lived in different places and times. The formal test was also consistent with multiple populations with independent origins gaining the ability to exchange essential genetic material effectively to become one species."

Passage B:

"While the formal test overwhelmingly favored the existence of a single LUA, this does not imply that LUA was ever alone. Instead, it was a member of the early microbial community.[4] Given that many other nucleotides are possible besides adenine (A), thymine (T, DNA only), guanine (G), cytosine (C), and uracil (U, RNA only), it is extremely unlikely that organisms descendent from separate abiogenesis events (that is to say separate incidents where organic molecules initially came together to form cell-like structures) would be able to complete a horizontal gene transfer without garbling each other's genes, converting them into noncoding segments. Similarly, many more amino acids are chemically possible than the twenty found in modern protein molecules. These lines of chemical evidence, taken into account for the formal statistical test by Theobald (2010), point to a single cell having been LUCA in that although it was a member of the early microbial community only its descendents survived beyond the Paleoarchean Era. With a common framework in the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have been feasible and may have been very common later on among the progeny of that single cell."

I hope you all appreciate this clarification! This is what the formal test favored. As Saey (2010) noted, a single LUCA with subsequent horizontal transfer among its descendents is anywhere from 102860 to 103489 times more likely than separate abiogenesis events coincidentally having the same nucleotide and amino acid framework so as to be able to partake in horizontal transfer without turning each other's genes into jibberish. The statistical test by Theobald (2010) reaffirms that statistic. The Mysterious El Willstro (talk) 18:42, 1 July 2013 (UTC)

Problem at Organism[edit]

The article at Organism contains material about the last universal ancestor that has been removed from this article, namely whether there is significant scientific debate about the existence of an LUA. See Organism#Was there a universal ancestor?. Should this article mention that there is a minority opinion held by the religiously motivated "intelligent design" advocates? --Bejnar (talk) 22:59, 11 December 2013 (UTC)

The point about lateral gene transfer making it difficult to pinpoint the LUCA is a good one and definitely relevant to this article. Opposition from the the ID crown would only be relevant to the degree there are relevant good sources for it. Petter Bøckman (talk) 08:07, 16 December 2013 (UTC)
It would be extremely difficult to "pinpoint" LUCA in the sense of reconstructing its exact genome. Horizontal gene transfer does make that task even more difficult. Even with horizontal gene transfer, though, the odds that LUCA existed are astronomically in favor. 103489. Horizontal gene transfer does not negate the existence of a single ancestral cell at some point; it only pushes back the date when that cell would have lived even longer ago. This is what Theobald (2010) clarified, truly a landmark paper.
If you're talking about LUCA being difficult to pinpoint, that is true. If you're talking about the existence of LUCA, however, the math definitely vouches for its existence. The Mysterious El Willstro (talk) 04:44, 21 December 2013 (UTC)
No, I was not discussing the existence of LUCA, I was as you suggested refering to the time of existence (though obviously not clearly enough). I suggest wording an entry something like this: "Transfer of genetic material between cells (horizontal transfer) makes it very difficult to pinpoint both the exact genetic the LUCA, and pushes the time of its existence back.", or something to that effect. Petter Bøckman (talk) 14:10, 27 December 2013 (UTC)
Ah, I see your point there. The Mysterious El Willstro (talk) 04:36, 27 March 2014 (UTC)

Is there debate?[edit]

I gather that the following is not a fair characterization of Dr. Doolittle's work: Uprooting the Tree of Life by W. Ford Doolittle (Scientific American, February 2000, pp 72-77) contains a discussion of the Last Universal Common Ancestor, and the problems that arose with respect to that concept when one considers horizontal gene transfer. I do not have access to Scientific American, so I cannot make a determination. If there is non-pseudoscience debate, should we not include it? --Bejnar (talk) 00:01, 12 December 2013 (UTC)

Any legitimate/non-pseudoscience debate about LUCA's existence ended in 2010, with a landmark paper already cited in this Article. Horizontal gene transfer does not cancel out the existence of LUCA; it only pushes back the date when LUCA would have lived. This was the conclusion of a paradigm-setting paper, and you're referring to a paper from 10 years before that.
As Theobald (2010) calculated from the genetic record (and in particular the universal use of the same genetic code, same nucleotides, and same amino acids), the factor in favor of LUCA's existence is 103489. As you know, 103489 is 1 with three thousand four hundred eighty-nine 0's after it! That is the number of times more likely that LUCA existed rather than not. The Mysterious El Willstro (talk) 21:14, 13 December 2013 (UTC)

Still confusing with Ur-organism[edit]

//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)

  1. ^ Marshall, Michael, Life began with a planetary mega-organism, New Scientist .
  2. ^ Cavalier-Smith, Thomas (2006), "Rooting the tree of life by transition analyses", Biology Direct 2006 (1:19): p11,13, doi:10.1186/1745-6150-1-19, PMID 16834776 
  3. ^ "Bergey's Taxonomic Outlines: Volume 5 - The Actinobacteria" (PDF), Bergey's Manual Trust, 2009  Unknown parameter |name= ignored (help)
  4. ^ Cite error: The named reference theo was invoked but never defined (see the help page).