Talk:Archaea/Archive 4

Number of Phyla
The introduction to this article currently states : "Archaea are further divided into four phyla".

Five phyla are listed in the box to the right. Looking at the individual articles, one states :"Thaumarchaeota are a newly-proposed phylum of the Archaea".

The current classification section states : "estimates of the total number of phyla in the archaea range from 18 to 23, of which only 8 phyla have representatives".

This field is obviously in flux, and I am not a SME.

I suggest that someone rewrite the introductory statement, so that there is at least a hint that the number of phyla is not precisely four. —Preceding unsigned comment added by 75.52.224.9 (talk) 22:04, 11 March 2009 (UTC)


 * Good point, thank you. I've added a note to this effect to the lead. Tim Vickers (talk) 00:58, 12 March 2009 (UTC)

Morphology
I was just wondering why there was no mention in this seciton about Thermoplasma or Ferroplasma which do not have cell walls and instead resemble more of an ameboid shape http://microbewiki.kenyon.edu/index.php/Image:Thermoplasma_2.jpg Additionally the second paragraph of the introduction has this odd statement "Generally, archaea and bacteria are quite similar in size and shape," when the morphology section directly contradicts this statement.--Jonthecheet (talk) 19:47, 16 March 2009 (UTC)


 * True, those species are discussed in the section on "cell wall and flagella", but they should also be added earlier. Tim Vickers (talk) 15:55, 14 April 2009 (UTC)

Bacterial Flagellum evolved from Type III secretory protein??
The article makes this claim when contrasting bacerial and archaean flagella. I've only read the abstract of the reference provided, but it looks like it only discusses the archaean flagellum, not the evolution of the bacterial flagellum. I always thought that it was believed that the Type III secretory protein evolved from the flagellum, not the other way round, because its only use is in pathogenicity and so it must have evolved after the organisms they parasitise whereas the bacterial flagellum is found in a wide range of bacteria from earlier on. I've only found 1 rather old reference to support this: Nguyen L., Paulsen I. T., Tchieu J., Hueck C. J., Saier M. H. Jr. 2000. Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnl. 2(2):125-44 (freely available here: ) Can anyone here confirm if this is the current consensus? If so, perhaps the article should be changed. —Preceding unsigned comment added by 79.64.178.86 (talk) 14:05, 14 April 2009 (UTC)


 * Yes, it looks like it is accepted that the bacterial flagella and the type III secretion system share a common ancestor, but the function of that ancestor (flagella or secretion system) is controversial. I've reworded the article a bit and added two references. Tim Vickers (talk) 15:53, 14 April 2009 (UTC)

Archaea don't do Anammox
I removed the words in energy metabolism that is mistakenly citing articles about Archae being involved in Anammox.

REMOVED: in anammox metabolism

Riennn (talk) 14:01, 9 June 2009 (UTC)


 * See Talk:Archaea above, I thought this had been corrected already. Tim Vickers (talk) 16:15, 9 June 2009 (UTC)

Thanks, I missed that, but it had not been fixed indeed. Archaea somehow contribute indirectly to anammox by feeding it with NO2, in the same way bacterial ammonia oxidizers do. I think it is out of scope here, if we start speaking about the fate of the product of ammonia oxidation by Archaea, this article would have to include a paragraph about importance of Archaea in removal of nitrogen from aquatic ecosystems. I will try to include all this in the denitrification article, which needs serious additions. Riennn (talk) 06:19, 10 June 2009 (UTC)


 * That sounds good. Would it also be possible for you to check this article over again to see if there are any other errors? Although I am a microbiologist, I'm not an expert on Archaea and might have got a few other things wrong. Tim Vickers (talk) 16:36, 10 June 2009 (UTC)

I certainly can do this although I am not an expert either... I don't think anyone can pretend being an expert on archaea I've been thinking about a person to ask to read it through... Riennn (talk) 05:16, 11 June 2009 (UTC)

Image of plankton in the oceans
I do not see any plankton in the image. Is the plankton blue or yellow? —Preceding unsigned comment added by 83.24.23.199 (talk) 07:10, 5 July 2009 (UTC)


 * They are the parts in light green. Tim Vickers (talk) 17:10, 5 July 2009 (UTC)

Edits /27
>If you believe there is such an error, please present it on the Talk:Archaea page

1:'"Although archaea have, in the past, been classed with bacteria as prokaryotes, this classification has been described as outdated, since it fails to distinguish between the three very distinct domains of life"

>three very distinct domains of life< are "new product" of new classification, not the reason to update the classification. In other words, until new classification was introduced, the stated fault ("since it fails") was nonexistent.

Common example : John Sulfolobus & Ann Escherichia: Although John married Ann, this marriage was outdated, since they fails to distinguish they are divorced.

Anyway this sentence was redundant. It duplicate better written information in : In the past they were viewed as an unusual group of bacteria and named archaebacteria but since the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, they are now classified as a separate domain in the three-domain system.


 * It is not redundant, as the prokaryote/eukaryote "dichotomy" is still commonly-seen. Tim Vickers (talk) 14:52, 28 August 2009 (UTC)

2 "Archaea are further divided into four recognized phyla."
 * Infobox list five.
 * Only two phyla are unquestionably accepted.

Xook1kai Choa6aur (talk) 05:08, 28 August 2009 (UTC)


 * I was following a 2005 review for this taxonomy, so this does not include the proposed (but not accepted) phylum of Thaumarchaeota from 2008. What source disputes the classification of Korarchaeota and Nanoarchaeota as phyla? Tim Vickers (talk) 14:52, 28 August 2009 (UTC)

Possible error in terminology
"These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms". My problem here is with the word *subkingdom*. In my amateur layman understanding, the groups Archaebacteria and Eubacteria must have been regarded either as kingdoms or as something higher, bigger than kingdoms, which would then be something like superkingdoms or megakingdoms - which is why, as I understand, we now work with domains. In any case, Urkingdom or Urkönigreich can never mean sub-kingdom, as Ur refers to something either older or greater than the word it precedes. Duchiffre
 * It wasn't Woese and Fox who treated them as subkingdoms. That issue was the result of other authors sometimes placing the groups at the level of subkingdom within the kingdom Monera.  Woese and Fox used the term "Urkingdom" instead, which later came to be called "Domain", to emphasize that they were something more than the traditional kingdom.  So there is not an error in terminology, as such, merely an unclear wording of the article text. --EncycloPetey (talk) 04:20, 25 September 2009 (UTC)

Ambiguous sentence
"Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the Archaea,"

does this mean to say that up to 15% of the genome is unique, or up to 15% of the proteins created by the genome are unique (e.g. it creates "pseudoglobin" whereas no known eukaryte genome produces this protein) (and thus, presumably, much more than 15% of the genome is unique)? As worded, it seems to refer to the latter, but it also seems from the context that it is supposed to refer to the former. Whichever it is, I think it needs to be made clearer. Kevin Baastalk 20:14, 3 December 2009 (UTC)


 * It did refer to proteins, so the literal meaning was the one I intended. I've reworded the context a bit to make a smoother transition. Tim Vickers (talk) 20:25, 3 December 2009 (UTC)


 * Yeah, that's much clearer. Thanks.  FWIW, I was curious as to whether one could make an argument for multiple origin (life starting in multiple places independently) based on variations in genomes at the base of the phylogenetic tree.  So I wanted to know how much of the genome was different.  I still don't know, but since that sentence does refer to the proteins, it could be quite a bit. Kevin Baastalk 15:40, 4 December 2009 (UTC)


 * Out of curiosity I just looked up "pseudoglobin", turns out it's a real protein (pseudoglobulin). Oh geez, you can't shake a stick w/out hitting one! Kevin Baastalk 15:43, 4 December 2009 (UTC)


 * One current idea is that life emerged out of a set of "replicators" that engaged in extensive horizontal gene transfer, making the "root" of the tree of life more of a basketwork than a single point. See this review for more details. Tim Vickers (talk) 17:47, 4 December 2009 (UTC)


 * Thanks. That was my argument that spurred my curiosity: that at such an early stage of evolution gene transfer would be ubiquitos so by definition of "species" you would have only one species.  But then i recalled that "speciation" can mean that even though they CAN genetically reproduce they are separated geographically enough such that they DON'T.  i'm a little fuzzy on the subtleties of that definition but in any case it brings up an interesting question: where they separated geographically enough such that they didn't; did there actually end up being a few baskets or just one; was the weaving above or below the percolation threshold?  One way to approximate the answer would be to compare the amount of genome variation in the earliest known (non-ubiquitiously reproducing) organisms.  Hence my curiosity.  The paper you referred me to does a good job of reminding me that it's not that simple.
 * Either case I was curious if the basis of my argument was valid; if my ubiqiuotos gene transfer in primordial organisms idea was scientifically credible. i didn't think I would find an answer to that very easily, but there it is!  Thanks!  Kevin Baastalk 20:24, 14 December 2009 (UTC)
 * - I love being right! (still curious if it was ubiquitois. I think it'd be pretty cool if it wasn't (if there are two "origin(s) of life")!)Kevin Baastalk 16:46, 1 February 2010 (UTC)

Tranlation and transcription
The navigation box for gene expression (akin to an book index for the topic) (link: Template:MolBioGeneExp) was edit some time back to include archeal translation and transcription, two pages that do not exist. As several months have passed, it is clear that the edit was for form as the other two domains had respectiove pages. Could an archean microbiologist add these pages if possible or redirect them correctly (I would assume to eukaryotic transcription and to prokaryotic translation). Thanks --Squidonius (talk) 13:21, 15 December 2009 (UTC)

Odd Chemical Claim
"Ether bonds are chemically more resistant then ester bonds, which might contribute to the ability of some archaea to survive at extremes of temperature and in very acidic or alkaline environments."

This doesn't make sense: why would a less chemically resistant bond increase survivability? Surely it should be "Ester bonds are chemically more resistant then ether bonds..." Hasname (talk) 17:56, 19 May 2010 (UTC)


 * "Which" here is referring to the increased chemical resistance. I'll reword this to be clearer - ""Ether bonds are chemically more resistant then ester bonds, this increased stability might contribute to.." Tim Vickers (talk) 19:34, 19 May 2010 (UTC)

I was having a really dense moment, confusing esters and ethers :s. Sorry to waste your time.

Hasname (talk) —Preceding undated comment added 20:33, 19 May 2010 (UTC).

Edit request from Mikejones2255, 11 June 2010
spelling error: under "Structure, composition development, operation", the first bullet point under membranes, it reads"... In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are chemically more resistant then ester bonds...." The "then" in the last sentence needs to be "than."

Mikejones2255 (talk) 11:50, 11 June 2010 (UTC)


 * I've made the change, thanks for spotting that. Mikenorton (talk) 12:07, 11 June 2010 (UTC)

Copy-edits
Copy-edits complete. Reduced word count by ~20%. Enjoy. Lfstevens (talk) 02:22, 12 June 2010 (UTC)

Copy-edits
Copy-edits complete. Reduced word count by ~20%. Enjoy. Lfstevens (talk) 02:43, 12 June 2010 (UTC)

Challenging the antiquity of Archaeans
Tim, I have just finished reading two articles by Thomas Cavalier-Smith in which he puts forward a very convincing case for the relatively recent emergence of Archaea (only 850 mya!!). In his Neomuran hypothesis he proposes that archaeabacteria and eukaryotes are sisters, rather than archaeabacteria being ancestral to eukaryotes. In addition to making a number of convincing arguments based upon molecular and cellular data, he also points out that there is no definitive paleontological evidence for archaean or eukaryotic fossils prior to 850 mya. He also notes that steranes which have been used as biomarkers to indicate the presence of eukaryotes 2.7 bya is unreliable due to the presence of these molecules in Arabobacteria and several other Eubacterial species. His analysis of how quantum evolution distorts the supposed "molecular clock" and the cladistic and phylogenetic conclusions drawn from such techniques is quite compelling.

I have long admired the work of Woese, Margulis, Schopf and others working on the origin and evolution of early life but these articles have forced me to radically reconsider my former understanding on these issues. In many ways Cavalier-Smith has struck at the heart of many burning questions and contradictions in the view put forward by the mainstream of the biological community. At minimum, I would think that these ideas deserve space in this article on Archaea. I would greatly appreciate your feedback on these issues before making any additions to this article.

Selected Articles:

This issue of Philosophical Transactions is dedicated to the topic... http://rstb.royalsocietypublishing.org/content/361/1470.toc

Thomas Cavalier-Smith - http://ijs.sgmjournals.org/cgi/reprint/52/1/7 - The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification - International Journal of Systematic and Evolutionary Mircobiology (2002) 52, 297-354

Thomas Cavalier-Smith - http://ijs.sgmjournals.org/cgi/reprint/52/2/297 - The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa - International Journal of Systematic and Evolutionary Mircobiology (2002) 52, 297-354

Jtwsaddress42 (talk) 19:32, 4 July 2010 (UTC)

Medo
In the section 'Current classification' a sentence starts "Most of the culturable medo". The word 'medo' is not in the Oxford or Cambridge online dictionaries. What does it mean or is it a typo? It seems surprising that an article of the day should use a word so obscure it is not in standard dictionaries. Dudley Miles (talk) 19:59, 10 January 2011 (UTC)
 * It was added by an anonymous user without comment. I've removed it. mgiganteus1 (talk) 20:39, 10 January 2011 (UTC)

Spore versus endospore
Okay, it's kind of a nit. But the use of "spore" in the lead section clearly refers to endospores, yet it links an article that heavily emphasizes reproductive spores and barely mentions endospores at all. I prefer the more specific term. Yaush (talk) 22:58, 10 January 2011 (UTC)
 * The more specific term applies to a single order of bacteria. The point of the sentence in the article is that archaeans do not produce any kind of spore, neither bacterial-type spores nor eukaryotic-type spores.  Linking to endospore would thus be far too specific for the article's content. --EncycloPetey (talk) 23:31, 10 January 2011 (UTC)

First sentence

 * "The Archaea are a group of single-celled microorganisms with no cell nucleus nor any other membrane-bound organelles."

The first sentence is a poor definition. It reads (to a layman) like any arbitrary group of microorganisms is called an "Archaea." It should be defined as a category of microorganisms, not a group.129.10.173.73 (talk) 23:05, 10 January 2011 (UTC)
 * Only the taxon label Archaea is a category. This article is about the organisms that belong to that category, not about the category itself.  The category Archaea has a place on Wikispecies, but we don't generally write articles about such categories in an encyclopedia. --EncycloPetey (talk) 23:29, 10 January 2011 (UTC)


 * That does not make sense. The article on Eukaryotes or Cordata is about the category as well as all the similarities shared between subcategories of the category and the individual species, as well as their differences and differences from other categories. Similarly for Archaea. -Pgan002 (talk) 06:40, 28 February 2011 (UTC)
 * No, the articles you meantioned are about the collected group of organisms, the similarities and differences between those groups of organisms. The category is an artificially constructed name and arbitrary circumscription, with a history of who coined the name, where the name was published, and when.  A cat can walk into a room, yes?  But if you define "cat" as a "category" with certain characteristics, then that clearly doesn't make sense, because a category does not walk into a room.  See the difference? --EncycloPetey (talk) 05:47, 5 January 2012 (UTC)

Split Article
I recommend this article be split, because it is about 90KB, and it should be split in 2 or 3 sections. Aerosprite the Legendary (talk) 02:51, 2 February 2011 (UTC)

Copy-edit of sentence under "Relation to Eukaryotes"
Under section "Relation to Eukaryotes", this sentence can be improved
 * "The leading hypothesis is that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure"

Is it correct to say the following:


 * "The leading hypothesis is that the ancestor of eukaryotes diverged early from Archaea, and that eukaryotes arose through fusion of an archaean and a bacterium, which became respectively the nucleus and cytoplasm of the Eukaryote cell. ... "

-Pgan002 (talk) 07:11, 28 February 2011 (UTC)


 * Domain names function in English as weak proper nouns, just as kingdom names do. Such weak proper nouns prefer use of the definite article. --EncycloPetey (talk) 05:41, 5 January 2012 (UTC)

New Domain - sentence does not compute
The following sentence - referring to PCR - is ambiguous and in some readings, tautologous.


 * This allows the detection and identification of organisms that cannot be cultured in the laboratory, which generally remains difficult.

What exactly "remains difficult" ? Allowing? Detecting? Culturing? And if it is now allowed, why still difficult?

And why is any remaining difficulty relevant to the existence of the New Domain?

Please consider rewording, or maybe just drop the last clause.

[But thanks for a really interesting article] Shannock9 (talk) 14:20, 2 April 2011 (UTC)

Candidatus formatting
The newly added section on Phylogeny includes several Candidatus forms. They are currently formatted as:
 * 'Candidatus Micrarchaeum acidiphilum'

However, per the Candidatus article, it looks like they should be formatted as:
 * "Candidatus Micrarchaeum acidiphilum"

I'm not an expert, so I will just note this here and not change anything. -- Donald Albury 00:57, 5 January 2012 (UTC)

"Prokaryotes are obsolete" - POV?
This article includes the assertion that:
 * "In the past [Archaea] had been classed with bacteria as prokaryotes (or Kingdom Monera) and named archaebacteria, but this classification is regarded as outdated."

This assertion is supported by a reference to an article in Nature [May 2006] by Dr. Norman Pace. Several microbiologists have expressed disagreement with Dr. Pace's ideas (e.g. William Whitman; Michael Dolan). I have seen no sign that the wider microbiological community is abandoning the term "prokaryote". This assertion may therefore raise a POV issue.

In Nov 2010, I (quite gently) addressed this by softening the assertion to read "...this classification is regarded by some as outdated."

This edit was reverted (deliberately or accidentally) by user Pot in April 2011, as part of a larger and well-executed "tidy up" edit. Pot does not appear to be a subject matter expert (no offence intended - neither am I!), so it is my intention to re-apply my original edit unless someone objects here, providing citable evidence that the term "prokaryote" is now regarded as obsolete or outdated by a majority of the relevant professional community. FredV (talk) 16:39, 5 January 2012 (UTC)


 * Is it perhaps proper to say that "prokaryote" as a clade or synonym for Monera is outdated, but is still valid as a grade. Now, is there a reliable source that says something like that? -- Donald Albury 22:07, 5 January 2012 (UTC)


 * The statement in question pertains to classification of a formal group called prokaryotes, not to usage of the informal morphological description of prokaryote. It is the classification that is outdated, and the sentence clearly says that.  You haven't demonstrated that this is not the case, and you seem to have misconstrued the meaning of the original sentence.  It is the same as the issue of the term "algae", which is no longer used as part of any formal classification, but is still used in morphological and ecological contexts.  It's not the term that's obsolete, but merely the classification. --EncycloPetey (talk) 02:47, 6 January 2012 (UTC)


 * I take your point. I had read "classed" as more or less synonymous with "grouped", rather than "formally classified". Since I may not be the only person to make this assumption, I will edit the passage to make this clearer. On the wider issue of rigorous cladistic classification at the domain level, I believe that evidence of a high degree of horizontal gene transfer during the early divergence of the domains, together with uncertainty regarding the precise nature and timing of the evolution of the eukaryotic cell, may render "classical" cladistic classification difficult - or even impossible. This would lend more weight to the retention of "useful" grade-like groupings such as "prokaryotes" (I do not agree with Dr Pace's argument that "prokaryotes" can not be reasonably well defined - but that is a much more complicated argument, and is probably off-topic on this page). FredV (talk) 12:12, 6 January 2012 (UTC)

In origin & evolution section, "the term prokaryote's only surviving meaning is "not a eukaryote", limiting its value" - surely prokaryote still means not having a nucleus!? Fig (talk) 17:31, 19 October 2013 (UTC)
 * Yes, I agree. There is disagreement over whether a formal rank should be assigned to the group or not, but the informal term still has a clear meaning regardless of this. Morphologically there is a clear difference between pro- and eukaryotes. Peter coxhead (talk) 00:59, 20 October 2013 (UTC)

genuinely
"to work out which prokaryotes are genuinely related to each other" what about "genetically" rather than "genuinely" ( Martin |  talk • contribs 04:21, 16 May 2012 (UTC))
 * "genuinely" is certainly an inappropriate word. Since the dominant hypothesis of modern biology is that all organisms are related to each other, "genetically" is also redundant (as is the simple, and preferable "to work out which prokaryotes are related to each other"). The actual objective is "to work out in what way different prokaryotes are related to each other". Now that you have pointed this out, I will modify the article accordingly. FredV (talk) 09:06, 16 May 2012 (UTC)

Relationship to other prokaryotes
I’ve been trying to make the recently added section “Relationship to other prokaryotes” more concise and less repetitive. (I also think this might be undue weight on a particular hypothesis, since this person seems to think the Archaea are not a separate domain. Perhaps this view should only be cut down to a sentence or two – I’m not sure how much weight it should be given).

(Interjection – the argument actually doesn’t make sense to me anyways. Of course the antibiotics for which archaea are resistant but bacteria are not will be ones that act on genes that are different between archaea and bacteria. If they acted on genes that were not different, then both groups would be sensitive. And any competitive selective pressure will promote colonization of new niches – there is no reason to think that antibiotics are special in this regard.)

Anyways, my most recent edit involved making a table summarizing the characteristics of Archaea and the other domains, so that I could replace the lists that were inserted into the text. I also added a few more characteristics, as well as citations. This is the first time I’ve made a table, so please let me know if there’s anything I could have done differently.

I didn’t remove any actual content in my first two edits (as I commented in the edit summary). Even now, almost all of the information is actually still there despite the large change in size. This time, though, I did remove a number of things that look to be either personal opinion or not necessary to the overall point (e.g. “some Archaea” showing positive Gram stains is not evidence for a link between Archaea and Gram positive bacteria, because the rest of them show negative stains). I then moved a couple of sentences on one of Woese’s proposals upwards, since he is already being discussed above, and added a few other phrases as well.

The section also wasn’t using citations properly – a number of them didn’t address the conclusions they were cited for, one didn’t link to an actual page, one was from a philosophy paper, etc. Three citations were being used to support the statement that Gram positives and archaea share the characteristic of having a single lipid membrane (I just left one); four citations were being used to support what was previously the third last sentence in the section (I only have access to two of them, but neither seemed to support the statement – I removed those two, and it would be great if someone could check the others); etc. I also removed a sentence from the section above (added by the same editor) for which the source was another wiki, and which made a slightly different claim from the one sourced here (besides which, I think the statement itself was a non sequitur)... There’s also quite a few that I didn’t have time to check.

I still feel that there should be more changes, but that will probably be enough for me, at least for now. I also think an expansion to the following section (which is the mainstream view, yet is still much shorter even after my changes) would also be in order. Arc de Ciel (talk) 09:50, 22 May 2012 (UTC)

Domain
The important fact that the group of organisms known as Archaea constitute a domain is currently only implicitly presented in the second sentence of the lead:
 * The Archaea ... are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon").

This is, in my opinion, insufficiently conspicuous. Additionally, the word "this" in "this domain" has no antecedent – which domain? none has been mentioned before. To address this issue, and suspecting that not all readers will know that in the context of biology the term "domain" has a specific meaning related to the taxonomy of organisms, I expanded the lead to:
 * The Archaea ... are a group of single-celled microorganisms, constituting a domain in the taxonomy of organisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon").

However, this was reverted with edit summary rationale: new wording is redundant; all domains are in the taxonomy of organisms. What do others think – just redundant, or an actual improvement? --Lambiam 10:21, 22 July 2012 (UTC)


 * I agree that Archaea being a domain needs to be explicitly stated, especially as many readers will have been thought in school that Archaea(-bacteria) are not a domain. I'm not sure on the wording, perhaps something like:
 * The Archaea ... are a domain of single-celled microorganisms. A single individual or species is called an archaeon (sometimes spelled "archeon").
 * Perhaps someone else can come up with something better. The current wording, referring implicitly to "this domain" without saying that the Archaea constitute a domain, definately needs improvement. 82.139.81.212 (talk) 12:04, 22 July 2012 (UTC)

Please look at the second paragraph, which is entirely about the classification of the domain. The status of domain does not need to appear in every paragraph. Rather, the article already has an entire body section on this issue, which in turn is summarized in the second paragraph of the article summary. As the article currently stands, the first sentences describe the organisms that are members, to describe what they are like, and then the second paragraph describes the grouping, explaining how it differs from other such groupings. The above proposals would conflate this distinction by trying to discuss both the taxon and its member organisms all at once, which is more likely to confuse readers than to assist them. --EncycloPetey (talk) 21:09, 22 July 2012 (UTC)
 * The lead of an article is not "every paragraph". There is a reason why our guideline states that the lead should be a summary of the article's most important aspects: you should not assume that the reader will read beyond the lead. Archaea being a domain is one of the most important aspects the readers should take away from consulting the article, and I maintain that this should therefore be explicitly stated in the lead. In your reaction you further completely ignore the issue that the word "this" has no antecedent, making the lead crappy prose. --Lambiam 22:33, 22 July 2012 (UTC)
 * The second paragraph of the lead is part of the lead. Did you not understand that in what I said?  The lead is not always a single sentence or a single paragraph, but consists of the entire summary section before the article.  My point was that we do not need to summarize everything in a single sentence or in a single opening paragraph.  We can spread the information out for clarity rather than dumping it all on the reader at once.


 * I did not ignore the issue of "this" having no antecedent; I knew your statement was in error. If you look at the grammar, "this" is used as a demonstrative determiner before a noun, and therefore it does not require an antecedent of its own.  Demonstratives require explicit antecedents only when they function as pronouns, and not when they function adjectivally.  In this case, it is domain that needs an antecedent, and it has one: the group Archaea.  As a clarifying example, consider: "Albania is a country in the Balkans.  This nation is home to the Albanian people."  There is no problem here with a missing antecedent, right? In the example, it is clear from context that "this nation" refers back to Albania, the subject of the preceding sentence.  Neither is the switch from "country" to "nation" a problem because the two words are near synonyms.  The current Archaea article begins in a precisely parallel fashion, with "group" and "domain" set in parallel, so that it is clear from context that both words refer to the same collective group, the Archaea.  The key to writing good prose is using all the available tools, including context.  --EncycloPetey (talk) 22:46, 22 July 2012 (UTC)
 * If someone writes, "Buy this!", it only make sense to the reader if they know what the word "this" references. If someone writes, "Buy this book!", it only make sense to the reader if they know what the noun phrase "this book" is meant to reference. In either case, the context should make clear what the referent is. I am fairly convinced that a substantial fraction of our readers, and a majority of those who have no background knowledge of biology, do not know that the term "domain" can reference a taxon. The common meanings are always some realm, range, or region; none of these meanings could normally reference "a group of organisms". Thus, many readers, and in particular those who are most in need of the knowledge we try to impart through the article, will fail to understand what the referent is of "this domain". --Lambiam 20:18, 23 July 2012 (UTC)
 * But your comment is unrelated to the question at hand. The article does not say anything like "buy this".  Rather, it says "this domain".  The noun "domain" exists in the phrase, just as you say it should, so I don't see the problem.  Now, if the sentence left out the would domain, forcing "this" to act as a subject, then you'd have a valid point.  However, "this" is not functioning as a subject; "domain" is.  And clearly, if "domain" refers to something, there is only one sentence and one subject before it, so there can be no ambiguity.  "Paris lies on the river Seine.  This city..." leaves no doubt that "this city" refers to "Paris". Even if an unfamiliar city name were used, it would be immediately clear from context that Paris is the city meant, and so it is clear in the present article that Archaea is the domain being discussed.  Again, context is key, and the context is there.  If you believe my explanation (which I have now given twice) is faulty, then please show me where I have gone wrong.


 * You seem to be blending this issue with a separate one: the clarification of "domain", which is in fact a separate issue. Now, if an article says that "Fungi is a kingdom", it is clear from context that it is not the everyday sense of a political nation that is intended.  If an article says "the family Flacourtiaceae", then it is clear that it is not the everyday sense of a "family" meaning a unit of sblings, parents, and similarly close relatives.  We don't need to explain terms further when they are explained in context, and in this case the first sentence says "group" and then uses the term "domain", providing the context for the meaning of "domain".  The point is further explained in the second paragraph of the lead to the article, in case it was not fully understood in the previous sentences.  Since there is already ample context and explanation, why does more need to be added?  And if, as you say, our readers are lacking in knowledge of biology, how will adding the technical jargon "taxonomy" make anything clearer in the lead? --EncycloPetey (talk) 03:35, 24 July 2012 (UTC)


 * Take the following sentence:
 * " For seating, a long backless bench is used, so that the children can seat themselves at a free spot between two occupied ones. This also discourages the assumption of a slouched posture. "
 * Unless you are British and had school dinners, you are not likely to get what is referenced by the words "this form". For a U.S. reader, none of the common meanings of the word "form" matches what it is intended to reference.
 * If the text in our article were to say "the domain Archaea", or "Archaea is a domain", then I concede that it will be clear to the reader that the term "domain" is used here in a technical sense. However, the first sentence says "group" and then the second switches to the term "domain". Even if readers see that the word "domain" is used there in a specific technical sense (which, I believe, many won't), what is it that should make them see that they should equate this word "domain" with the earlier word "group"? Suppose the term chosen by Woese had been "region". Then we would have had:
 * " The Archaea ... are a group of single-celled microorganisms. A single individual or species from this region is called an archaeon (sometimes spelled "archeon"). "
 * Would an unprepared reader understand that in the last sentence "this region" references "a group" from the first sentence? I think not; they would just think: "Huh? What region?" --Lambiam 10:17, 24 July 2012 (UTC)


 * The "form" example you've given would indeed be confusing to an American reader, but a large part of the problem is that the context in that example is buried in the structural complexity of the first sentence. In your example, the first sentence begins with a phrase that does not contain the subject, and concludes with a lengthy independent clause in addition to the main clause of the sentence.  It therefore hides the subject by introducing additional clauses and phrases.  Our article's first sentence is a simple sentence with a copula (linking verb).  There is thus only a single subject and its complement with no clutter.  A better example might be:
 * " The Edmonton is a disused hotel in the commercial district. This squat is one of many that the city plans to demolish. "
 * I believe that both in my example and in the current article itself, the context of the potentially unfamiliar sense is provided by the simple structure of the sentences used. If you still disagree with that point after this round of discussion, then I suggest we remove the term "domain" entirely from the first paragraph, and discuss a way of inserting it into the second paragraph, where the matter of the grouping is properly summarized.  I dislike the idea of using a jargon word in the opening sentence, rather than a more generally understood term such as "group", especially since that would leave open the question of whether "domain" meant a taxonomic group or a genetic region.  Yes, there is a different sense of "domain" used in genetics.  The current text gives "group" as context to resolve that issue, but dumping the term "domain" on the reader in the very first sentence obliterates any context, and the reader already has to contend with the visual insertion of pronunciation information there. --EncycloPetey (talk) 17:39, 24 July 2012 (UTC)
 * Would a simple compromise be "... this group (or domain) ..."? FredV (talk) 09:28, 26 July 2012 (UTC)
 * Relegating it to a parenthetical expression reduces the importance of "domain" in the text, implies that it is a 100% synonym of "group", and unnecessarily interrupts the flow of the opening paragraph. So, yes, it's a simple compromise, but it's also bad prose. --EncycloPetey (talk) 18:23, 26 July 2012 (UTC)
 * How about "The domain Archaea (...) is a subset of the single-celled microorganisms. A single individual or species from this domain...".
 * 1. 'Group' is laden with unwanted associations and the naive reader may wonder what the difference between a group and a domain is, so why introduce 'group' at all?
 * 2. If I understand the topic, 'subset' is accurate here, whether a taxonomic group or a genetic region is meant, and you do immediately go on to clarify the membership criteria you espouse.
 * BTW school dinners is itself British English - a US equivalent might be canteen lunches :) --Shannock9 (talk) 04:49, 28 July 2012 (UTC)
 * Actually "school dinners" is used in the US; I've never heard then called "canteen lunches" in any part of the US where I've lived.


 * The term "subset" introduces unwanted interpretation, as it implies that a domain is a subgroup of some larger taxonomic group. It isn't.  The highest rank in the entire classification of life on Earth is the rank of domain.  So, calling it a subset of something else is misleading.  Domains are not subsets of anything except Life (and that has no rank in taxonomy).  We used the word "group" in writing the introduction because it's a simple, everyday word that the reader will understand in the definition.  The taxonomic sense of "domain" is not likely to be understood by the reader, and that's why there is so much explanation of the concept later in the article.  Dumping a word like "domain" on the reader in the first sentence, when that word requires so much explanation itself, would not make for a clear definition.


 * The latest proposed rewording also introduces a problem that I've noted before in this discussion. We want to avoid entangling the idea of the domain as a taxon with the idea of the organisms themselves. To put this in the form of an example: the introduction to the cat article says, "The domestic cat...is a small, usually furry, domesticated, carnivorous mammal."  It doesn't say that it is a subset of carnivorous mammals, nor that it is a species (even though the domestic cat is classified as a species).  The technicalities of classifying an organism are separate from the description of that organism.  Now, Archaea is a much broader grouping of organisms, but it is no less a grouping than "cat".  The opening paragraph here is not intended to be about "membership criteria" any more than is necessary with any definition.  The problem with language is that "archaea" is the plural informal name refers to members and "Archaea" is the formal taxonomic name for the domain.  Capitalization alone distinguishes the two.  The same is true of "fungi" and "Fungi", "bacteria" and "Bacteria", as many other groups.  So, please keep in mind that combining "domain" into the first sentence actually changes the meaning from an informal description of the members to a formal diagnosis of the taxon.  I'd like to avoid introducing that problem. --EncycloPetey (talk) 06:06, 28 July 2012 (UTC)
 * Ok, I see why you don't want the word domain in the first sentence. You want to describe the target without "classifying" it.  [Though after you recent explanation I do wonder why the first sentence has Archaea rather than archaea.]  My problem, reading this as a nonspecialist is with the word group, which appears to be a classification (since I don't know the official hierachy, nor the distinction between description and classification) after which I'm given a conflicting classification in the next sentence.  So then I think perhaps group wasn't a classification, perhaps it meant "a physical clump of".  I cannot decide which it is and am left with a less than good feeling.
 * How about simply "The Archaea (...) are single-celled microorganisms."? That would be entirely consistent with your cat template and also with Fungus (note the singular).  Bacteria (and Dog) do use classificatory terms in the first sentence, but who's counting? --Shannock9 (talk) 07:46, 28 July 2012 (UTC)
 * IIRC, that was a possibility was discussed when the article was up for FA. The objection that was raised then (and with which I still agree) is that it then appears that the Archaea consist of all single-celled microorganisms, which is not the case.  We opted for "group" at the time, and your suggested "subset" attempts to get at that meaning as well.  I think that "subset" is less successful than "group", but some indication is needed that we are dealing with only some of all the possibilities rather than the entirety.  There may be another way to express this, but I've yet to figure it out or to find someone else who can. --EncycloPetey (talk) 19:29, 28 July 2012 (UTC)
 * Maybe this objection was invalid. "Gorillas are hairy animals" carries no implication that they are the only hairy animals, and leaving out any reference to "group" (or "subset" or "domain") does seem to "defuse" the problem. FredV (talk) 09:04, 31 July 2012 (UTC)

Genetic Code and Aminoacyl-tRNA Differences with Other Domains
Forgive me if this incorrect, but aren't there some significant differences between Archae and the other two domains with regard to the codon/amino acid pairings? It seems to me that this is one of the most striking points to be made in describing this domain, yet I see no mention of it. It also has implications for how life evolves and has evolved on earth beyond merely differentiating the Archae from the other domains. Hopefully an expert in the area could rectify this issue. — Preceding unsigned comment added by 84.73.178.51 (talk) 20:13, 25 August 2012 (UTC)

Woese's article in Sci.Am. Dec 2012
Carl R. Woese, Archaebacteria: The Third Domain of Life Missed by Biologists for Decades http://www.scientificamerican.com/article.cfm?id=archaebacteria-the-third — Preceding unsigned comment added by Shoshie8 (talk • contribs) 14:12, 1 January 2013 (UTC)

"Scientific Worldview Timeline" main section?
I don't know if this question would be better in some already established section on the Talk page - it's so big that I figured to just put it in a new section.. Would it be reasonable to put either a main section or in the lead paragraphs a one or two sentence description of *when* the idea of Archaea as a kingdom came into existence/acceptance?

The "worldview" I learned in high school in 1994-97 was of only three kingdoms: Prokaryotes, Eukaryotes, and Fungi. I don't know whether the idea of splitting off an Archaea kingdom from Bacteria was "around" at that time or not - I remember hearing about it at some point then I think. But I just read the statement on the Eukaryote page that Eukaryotes are actually closer to Archaea than to Bacteria, and had no idea of that. From the sources on that page, it looks like that idea "came to be" around 2000-2006 - but I have no idea whether it's made it's way into "newly-written" bio textbooks or not, or is still mostly just in the primary literature.

A lot of this is scattered throughout the Kingdom_(biology), so it may not belong here at all, even in the lead overview. Jimw338 (talk) 20:23, 27 February 2013 (UTC)

Three changes
I just made three changes to this article:

1. Deleted the ugly pronunciation respellings (PR). As I explained in the talk for Pronunciation respelling key, I don't like PR, and in that talk, kwami and CUSH explained why PR is undesirable.

2. Added an alternative singular, arch(a)ea, the singular that I prefer (using the same form for both singular and plural). In English there is a widespread shift among nouns of Greek or Latin origin that traditionally have singulars ending in -on or -um and plurals ending in -a, as follows (singular given first): -on/um, -a →  -a, -a  →  -a, -as (the lattermost plural being regular):


 * criterion, criteria →  criteria, criteria  →  criteria, criterias
 * bacterium, bacteria →  bacteria, bacteria  →  bacteria, bacterias

In the case of archaea and bacteria, I am in the second stage of the shift (bacteria, bacteria). I don't think this shift is something to be stigmatized, but a natural part of language change, regularization. English has too many irregular plurals.

3. I changed "may be" more than four phyla to "almost certainly" more than four. There are about about 15 kingdoms of eukaryotes, and eukaryotes are much bigger than archaea, so there should be much more diversity among the archaea. In fact, I wonder if the four recognized phyla of archaea should be upgraded to kingdoms.

Does everyone approve of my changes?--Solomonfromfinland (talk) 15:44, 16 May 2013 (UTC)


 * Not #3. At least in rank-based nomenclature, supraspecific taxa are created by human convention and do not exist in cases where these conventions have not been formulated. Peter Brown (talk) 16:11, 16 May 2013 (UTC)


 * I oppose #2—"bacterias" and the like does not reflect well on Wikipedia.—Kelvinsong (talk) 19:12, 16 May 2013 (UTC)


 * It's been weeks now—I've gone and removed the "archæa".—Kelvinsong (talk) 12:49, 7 June 2013 (UTC)

Neutral point of view on the phylogeny of the Archaea
I think that by presenting only the diagram from Ciccarelli et al. (2006), the article does not present a fully balanced, neutral account of views on the relationship between the three domains. As far as I can tell, this remains disputed, with three distinct hypotheses current, of which neither the Ciccarelli et al. (2006) version (three monophyletic domains) nor the Cavalier-Smith (2010) version (Archaea are recent) is the most commonly held view. I've tried to correct this via an addition to the article showing three possible versions of the phylogeny of the domains. Peter coxhead (talk) 13:27, 1 August 2013 (UTC)


 * I have removed the picture, because versions 2 and 3 aren't valid evolutionary trees. Contemporary groups must be at the same height. The most precise terminology is that any scientific debates on these issues are about which groups share common ancestry more recently and which of the descendant groups the common ancestor most resembled.  Sunrise    (talk)  19:22, 24 December 2013 (UTC)


 * Actually, I have removed the rest as well. This is going a bit further than what I'm completely confident with (I would need to spend a few hours reading the sources), but the text doesn't seem to make sense either. From the pictures (trying to interpret them into valid evolutionary trees), the different versions are trying to make claims about what the common ancestors resembled. This seems like approximately what the text is trying to say as well, but if so the content needs to be rewritten, e.g. if that is the only issue then the evolutionary trees will look the same. There is also e.g. version 2 calls Neomura paraphyletic but this is contradicted by the first sentence of the paragraph as well as by the picture.  Sunrise    (talk)  19:46, 24 December 2013 (UTC)

Ambiguity of 'archaean' when both geologic time and organisms are being discussed
In articles such as this, when it unclear whether one is talking about a primitive organism (Archaea) or an eon of geologic time (Archaean eon) the adjective 'archaean' can be ambiguous. To mitigate this ambiguity, I have changed most instances of 'archaean' referring to the organism to 'archaeal', which I think is less ambiguous because it seems to be rarely used in connection with the eon.CharlesHBennett (talk) — Preceding undated comment added 11:16, 3 March 2014 (UTC)

Introns
The article contradicts itself on the issue of introns in Archea. The table comparing domains says that Archaea and Prokaryotes have no introns. The Genetics section says Archaea have introns in some genes. I believe the latter is correct but I don't have a reference. — Preceding unsigned comment added by Jason.Rafe.Miller (talk • contribs) 00:04, 23 September 2014 (UTC)

Wrong Domain?
I'm no life scientist, but wouldn't "Halobacteria" be in the bacteria domain intend of Archaea? — Preceding unsigned comment added by 74.67.173.198 (talk) 01:31, 18 October 2014 (UTC)
 * No, just as pineapples are not apples. The name was given to the genus before it was known to be an archaean, and by the rules of naming organisms scientifically, it can't be changed simply because its relationships are now known to be different. --EncycloPetey (talk) 06:32, 18 October 2014 (UTC)