Talk:Three-domain system

36s ribosomal unit
''However, by comparing the 36S ribosomal subunit it is clear that Eukaryota are genetically closer to Archaea than Archaea are to Bacteria, suggesting an early evolutionary divergence between Archaea and Bacteria and a later branching of Eukaryota from Archaea. Chloroplasts and mitochondria which inhabit almost all eukaryota are known to have evolved from Bacteria.''

This misses the entire point of the criticism. If Bacteria are paraphyletic to Archaea, and Archaea paraphyletic to Eukaryota, then it's only natural that archaeans should have closer sequences to eukaryotes than bacteria do. So it doesn't support the three-domain system over the alternative two-empire-one-paraphyletic system, as this suggests. The 36S ribosomal unit info could still be valuable, but I'm not sure how to work it in. Josh

Typo?
I'm no biologist, but shouldn't the word "eukaryotes" in the first line read "prokaryotes"? Rbraunwa 00:27, 21 July 2006 (UTC)

It should; fixed. Josh

should it be "bacteria" or "prokaryotes"? just a doubt... av: march 30, 2009

Clean up terminology
I'd like to echo what this person says (below): please rewrite for the layman! Thanks!

I generally know about prokaryotes and eukaryotes, but I have no expertise in the field. I had to read the article several times to make sense of the terminology; it reads like one expert describing it to another, throwing around jargon loosely.

It would help to, 1) Clearly define the terms and their relationships to each other.  Also putting all the terms in the graphic would help tremendously by providing a quick reference.  2)  Simplify, simplify, simplify: Eliminate synonyms and re-use the same terms as much as possible. For example, just this phrase creates much confusion: "biologists like Mayr criticized him for over-emphasizing the uniqueness of the archaebacteria and ignoring strong genetic similarities between the groups" What are archaebacteria? Archaea? Bacteria? I looked at the graphic, but archaebacteria isn't there. I had to re-read the first paragraph (not a good sign) to find, ... originally called Eubacteria and Archaebacteria, which raised more questions: 1) They were originally called that: Are the terms obsolete? Why use them in the next paragraph? What are the proper terms? 2) Which term corresponds to what on the graph? Also, what exactly is a group? How does it relate to a domain?

I'm not asking for help -- I believe I figured it out. I'm asking that someone help the next non-expert reader. I would re-write it, but I'm not qualified.

Thanks, phrustrated in philly

Date Discrepancy
This article states that the Three Domain System was introduced in 1960. The article on Domains indicates 1990. Please correct the wrong one. Artworksmetal 18:51, 31 January 2007 (UTC)


 * For the record, that appeared to be vandalism and 1990 was correct. I fixed it before I saw this post. 66.92.53.49 22:12, 11 February 2007 (UTC)

Neither is fully correct. 1977 marked the birth of the essence of this taxonomy scheme Pagelm (talk) 01:13, 24 October 2011 (UTC)

Viruses
This is an interesting position. Viruses aren't considered a life-form therefore they do not belong to any of the three branches, but viruses themselves are defined as non-life because they depend on a pre-existing living organism to maintain themselves.... So viruses, deducing this logically, had to have evolved (come into being) after life-forms of some kind evolved; therefore viruses must have a starting point with one of the branches, they had to have been an offshoot of one of them and therefore a "branch off" of one of the branches. Can any one make an argument any other way? Nagelfar (talk) 03:05, 4 February 2008 (UTC)


 * There is a simple way to deal with this problem: the three-domain system applies to cellular life, and so viruses are excluded. There are some theories about DNA viruses playing an important role at the birth of the three domains (see Patrick Forterre, Proc Natl Acad Sci 103:3669-3674, 2006 doi:10.1073/pnas.0510333103), and are as ancient as the main cellular lineages, but I think that the question is outside the scope of this article (at least for its current size). Szentendrei (talk) 20:03, 5 February 2008 (UTC)


 * This point has been clarified more recently. Virus evolution - at least at the RNA/DNA sequence level has been too rapid for the standard evolutionary methods to resolve this problem completely. Having said that the current consensus is that viruses have co evolved with their hosts for most of their existence. Precisely when the viruses of these lines evolved seems unlikely to be answered in the near future. —Preceding unsigned comment added by 159.134.58.241 (talk) 15:54, 14 April 2008 (UTC)

Sure it was 1990?
Hi,

I am not an expert on the subject but I have a "gut feeling" the date 1990 might be a typographical mistake. Maybe it was meant to be something like 1890?

It's just my gut feeling... I've never studied this subject in depth but I was taught about this subjects in Middle School and I graduated from High School some 5 years ago, so my "gut feeling" is that 1990 is too fresh of a date for the theory to have been first presented and become world famous and be included in my school's Biology program (unfortunately I did attend a quite "backwards" school system... in Mexico... and I'd be surprised if they are so "up to date"). —Preceding unsigned comment added by 109.253.125.31 (talk) 13:37, 8 December 2010 (UTC)
 * Nope, it was 1990. It reached widespread acceptance rather quickly because it explains the realities better than any competing system. --Khajidha (talk) 00:59, 14 January 2011 (UTC)


 * I can't confirm when Woese published, but I CAN confirm that US high school textbooks described a Five-Kingdom system, did not distinguish Archaea from Bacteria, and did not recognize Domains as root-level taxa as recently as 1989. Though my observations probably count as personal research ;) --Raduga (talk) 08:12, 8 September 2011 (UTC)

It most certainly was not a concept proposed in 1990. In '77 Woese showed a phylogenetic tree based on 16S and remarked upon bacteria being divided into two groups (the traditional bacteria and the archaebacteria), which he called kingdoms (thus demoting the traditional kingdoms, including "animalia"). Science textbooks are often hideously out of date, especially those that upset the old system of order. -- — Preceding unsigned comment added by Pagelm (talk • contribs) 01:10, 24 October 2011 (UTC)

Discussion on whether to include a criticism section
Hi there. I can understand where the user Headwes is coming from in deleting the "criticism" section I've been trying to put up. Believe me, I do. I understand that 99.9% of scientists see no issue whatsoever with the 3-domain system. However, I don't believe that they've given it much thought, actually. The criticisms of Ernst Mayr (one of the most respected biologists of the 20th century) and the much less well-known Radhey Gupta, not to mention Thomas Cavalier-Smith, are real and I think they are pretty convincing, actually. But either way, they are real criticisms.

I'm not sure what you mean by "never amounted to anything." At first you were hesitant to include the section because I only put up one reference. I agree that one reference from an unknown scientist is probably not enough. But again I have to point out the prominence of Ernst Mayr and his absolute disdain for this theory. He published a completely devastating paper criticizing this theory of three domains -- why would that not be allowed in a criticism section, if we are being completely unbiased?

I am willing to work with you on the actual text of the section, but I think people have a right to know that not every scientist (and indeed, some prominent ones) are not on-board with this idea and still promote the 2-empire theory instead. I see no reason not to include a section detailing the real criticisms that have been brought forth. It's as if you want me to believe this 3-domain model is a fact when it is far from proven, despite its widespread acceptance.

Okay, so I've been reading up on POV forking on so forth (I've never edited Wikipedia before this article). It says the best way to include criticism is line-by-line inclusion without a "criticism" section. I think this would be a mistake for this article, because it would give undue attention to the criticisms. I'm not trying to debate the scientific consensus here (I agree there is one, even if I disagree with it), but only to provide resources for people to look into other points of view. It saddens me to see the three-domain hypothesis treated as fact when it is so poorly supported, imo. If you really think the criticism section is a bad idea, we at least need one or two sentences in the actual article proper to point people to the 2-empire theory (which has a much longer history of scientific acceptance than does the 3-domain). Would that be more acceptable to you? IMO, leaving the main article untouched is a better idea, and actually serves to support the theory more, but it's up to you since you seem so dedicated in deleting my section.

I beg you to read Gupta's work, as a side note. It is extremely convincing and well-supported.

Continuing some more... if we're going to do this line-by-line in the main part of the article, I'm going to tear into the concept of a "progenote" -- it was always ridiculous and even Woese has backed away from the idea. It's hard to imagine someone actually put that into the article. There is no backing for it whatsoever. These are the sorts of things we'll have to work out if you are still unwilling to let me have a simple criticism section. We'll have to debate the actual components of the 3-domain theory, some of which are easily disprovable. I don't think that simple popularity among scientists (who have no background in classification -- they really have no expertise here whatsoever) is enough to treat this very young idea as fact. The fact that it has become so prominent so quickly is a testament to the social power of molecular biology. I'm a molecular biologist myself. I understand the appeal. But once you look at classification systems more closely, I think you and many scientists would change their perspective on this. — Preceding unsigned comment added by Dowdcc (talk • contribs) 02:49, 23 November 2013 (UTC)

Ambiguous wording
The first sentence under the heading "Domain Archaea" seems ambiguous to me. The sentence reads: "The Archaea are prokaryotic, with no nuclear membrane, distinct biochemistry, and RNA markers from bacteria." The grammar and punctuation suggest a reading of the sentence that is contrary to what I as a layperson would expect the intended meaning to be. Specifically, the comma and "and" following "biochemistry" strongly suggest that the meaning of the final part of the sentence is that Archaea have distinct biochemistry (not distinct from anything in particular), and that they have RNA markers that come from bacteria. However, I would have expected the intended meaning to be that Archaea have biochemistry that is distinct from bacteria, and they have RNA markers which are distinct from the ones that bacteria have. As I say, this is a lay guess as I don't know what RNA markers are.

Whatever the intended meaning is, it is possible for the layperson to misinterpret it. If the latter meaning is the correct interpretation, may I suggest rewording the sentence to read: "The Archaea are prokaryotic, with no nuclear membrane, and biochemistry and RNA markers distinct from bacteria." Alternatively break the sentence into two sentences.

--Biirnats (talk) 05:30, 22 March 2020 (UTC)

I came to the talk section with exactly the same comment. I couldn't have expressed it as clearly as Biirnats.Jpipersson (talk) 16:29, 29 April 2020 (UTC)

Traded for a horse?
Eukarya has 5 kingdoms: Plantae, Protista, Animalia, Chromista, and Fungi [says Domain (biology)].

Bacteria looks like nil on wiki. Ditto for Archaea.

So, 7 kingdoms all-up? Or 5?

MBG02 (talk) 17:56, 29 April 2020 (UTC)

Caption to Tree image
--Whschirmer (talk) 18:25, 21 May 2021 (UTC) The caption to the tree image includes the statement: "It's now known to be grossly incorrect." What's the source of that statement? Does that mean the three-domain classification system is grossly incorrect? Is there a correct article to which one should be referred?

I noticed this too. Is it because it doesn't include horizontal gene transfer? That image is used within several articles on wikipedia. In any case, I think the statement of it being grossly incorrect needs to be clarified. 86.130.124.146 (talk) 17:33, 6 June 2021 (UTC)


 * Not sure what's going on here, but it seems that someone has seen to "fix" that problem by "correcting" the Woese et al 1990 tree using ... undocumented sources ... I think we call that WP:OR? Anyway, the tree is NOT Woese et al's, so the article with it blazoned at the head is now grossly incorrect. I don't know what would be best, but I would suggest that if people want to illustrate Woese et al as a piece of history, they provide that tree, warts and all; if they ALSO want to have a "correct" tree (whatever that might mean), then they provide a second (third, fourth, ...) diagram, citing it to a reliable source. All the best, Chiswick Chap (talk) 16:35, 8 October 2022 (UTC)