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Prokaryotes (from Old Greekpro- before + karyonnut, referring to the cell nucleus, + suffix-otos, pl.-otes; also spelled "procaryotes") are organisms without a cell nucleus (= karyon), or indeed any other membrane-bound organelles, in most cases unicellular (in rare cases, multicellular). This is in contrast to eukaryotes (also spelled "eucaryotes"), organisms that have cell nuclei and may be variously unicellular or multicellular. The difference between the structure of prokaryotes and eukaryotes is so great that it is considered to be the most important distinction among groups of organisms. Most prokaryotes are bacteria, and the two terms are often treated as synonyms. However, Woese has proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of the significant genetic differences between the two. This controversial arrangement of Eukaryote, Bacteria, and Archaea is called the three-domain system.
By these standards, prokaryotes and eukaryotes represent whole separate domains of organisms. Prokaryotes are organisms without membrane-bound organelles and almost entirely unicellular.
So a eukaryote isn't a prokaryote by this standard, because eukaryotes DO have membraine-bound organelles.
However, cladistics employs a system of taxonomy in which clades are defined by a grouping of characteristics that apply to all members of a group, without making exceptions (of course, there are exceptions to these lack of exceptions - tehe). Here's an illustration from Aron-Ra's excellent website on the topic:
According to this standard, any lineage (H-A) must belong to all parent branches. So A is a subset of B, C, D, E, F, G, and H, simultaneously.
Cladistics organizes life based on monophyletic groupings. Monophyletic refers to groupings of organisms who all share a common, ancestral population. So all animals have a universal common ancestral population, as do all chordates, vertebrates, and mammals.
As such, we're only interested in monophyletic groupings in that respect - groupings which AREN'T monophyletic have no real, taxonomic relevence.
As such, I'd propose the following:
Either Prokarya is a meaningless taxonomic term, or ALL life on this planet are, by definition, members of Prokarya, and thus, prokaryotes.
Linnaen taxonomy creates this sort of problem all the time. The problem is that it's entirely possible (and, indeed, literally all over the place) to have a subset of one group of organisms be at an equivalent or greater taxonomic placement than its parent grouping.
In this case, both Eukarya and Prokarya represent Domains in parallel. But evolutionary theory posits that eukaryotes are derived from prokaryotes. As such, this makes Eukarya a subset of Prokarya by the same logic H is a subset of that initial line in the picture above.
But, by the standards of taxonomy we apply to ALL groupings of organisms, Eukarya must STILL belong to Prokarya if Prokarya is a meaningful, monophyletic taxon.
What has happened is that "conventional" Linnaen wisdom has led to a definition/classification of prokaryotes that arbitrarily excludes daughter branches of that group. This is a standard that would be considered intolerable for any other grouping - but I'm not sure how many biologists would even agree with the logic I'm presenting here, despite, imho, my assertions being demonstrably true. The classic definition seems to prevail, despite the fact that we do treat Prokarya as a meaningful taxonomic grouping, and despite the fact that we hold that all life has universal ancestry in a prokaryotic population of organisms.
Edit - some added material for further clarification:
But I'm honestly not sure why. The primary objection seems to be that we're not prokaryotes based primarily on the definition of prokaryotes given above - this definition represents a consenus view of biologists, and since eukaryotes and all non-prokaryotic organisms fail to meet it, then that makes us not prokaryotes.
In cladistics, a given clade can't be monophyletic if excludes any descendent clades. As far as I know, most cladistic standards hold amphibians and all descendent terrestrial vertebrates as still belonging to a parent branch of Sarcopterygii (Stegocephlia in particular), despite the fact that they don't have all of the features of that original taxon (e.g. 2 chambered heart and fins). Similarly, mammals are usually held as being part of Synapsida despite the fact that the name "synapsid" refers to a feature which mammals no longer possess (a single temporal fenestra). Same logic for some of the descendents of Diapsida (snakes not having two temporal fenestrae), and so forth.
So, we already have many groupings in which features of that original grouping are lost or changed (fins to limbs, a chamber here or there for the heart, loss of fenestrae etc). But we still hold descendent branches as being part of the parent branches despite this.
And this logic perfectly mirrors what we find in eukaryotes, who are held as being descendents of prokaryotes, but have lost some of the defining features of prokaryotes (lack of true nucleus etc).
Note: further notes on horizontal transfer etc follow.
Last edited by mikeynov; 6th July 2005 at 07:32 AM.
The problem is with the standard rules of taxonomy, is that it relies on bifurcating trees - the nature of bacteria and the earliest organisms is such that this logic is inapplicable as a result of the masses of horizontal transfer and intracellular symbiosis. Prokaryotes are defined in such a way that Eukaryotes are simply not prokaryotes, this doesn't occur anywhere else in taxonomy.
it's not arbitrary at all, it is just because of the nature of the earliest and most basal forms of life, the methods that they use to replicate and the ways which they evolved. When one looks at taxonomy, one sees that all the descriptions that apply to a parent group also apply to the child groups, and this does not apply with the definition of prokarya. While the parents of Eukaryotes may have ultimately been prokaryotes, you cannot say that Eukarya are Prokarya, because the definitions simply do not match i.e. Eukaryotes by definition have a defined nucleus, and prokaryotes by definition do not.
In other words, Jet black feels that it makes some degree of sense that Prokarya is excluded from the logic we apply to all other clades of organisms.
In one sense, I do see his point - while I'm loathe to quote anything Mark Ramsey ever cited, I'll post the following picture for purposes of illustration:
What is being said here is that Prokarya has a means of reproduction in which there is heavy and frequent horizontal transfer of genetic material. This means that one prokaryote can send a portion of its existing genome to another prokaryote via conjugation.
However, prokaryotes not only duplciate their genetic information in this manner, they obviously spread it vertically too via binary fission. Note that both Archaea and the earliest eukaryotes (descendents of which are the modern day protists) also possess this capacity to spread genetic information horizontally.
And given this fact, I'm still confused as to why we couldn't apply the same basic logic to prokaryotes that we do to all other groupings of organisms.
While it would be difficult to classify organisms that contain horizontal transfer, applying this logic universally would almost certainly exclude both animals and plants due to their incorporation of prokaryotic elements endosymbiotically in the distant past.
Our basic standards of taxonomy do rely on vertical transfer - and for the most part, this largely holds (though there is evidence of horizontal transfer via virii and such throughout most of the domains of life which would put a bit of spin on all our taxonomy in that sense). The prokaryotic stock from which eukaryotes derived was at least partially the result of vertical transfer.
The basic logic of "groups within groups" holds insofar as eukaryotes really are a subset of prokaryotes. And, given this fact, it seems to me that we would still be forced to classify Eukarya as a subset of Prokarya.
Last edited by mikeynov; 6th July 2005 at 06:41 AM.
First of all, I object to the claim that prokaryotes are a single domain, and here is my justification for doing so. The three domains in life are regarded as the bacteria, archaea and Eukaryotes (nucleated organisms), which are thought to have descended from an earlier progenote (Woese 1977). These three domains are separated by much more fundamental issues than internal structure, in the chemistry of the organisms.
The problem with trying to claim that we are prokaryotes based on the logic presented in the OP is that prokaryotes describes a specific characteristic that eukaryotes do not posess i.e. free DNA and lack of various intracellular structures. It would be akin to claiming that because our ancestors are tree - dwellers, then so are we. It is far more correct to define the domains as suggested, into these three categories, which have their own common group, to which we all belong.
To further the argument, it was claimed in the original thread that because of this, we are bacteria, and there is clear evidence against this. currently extant bacteria have a number of features that distinguish them from the other two domains, archaea and eukaryotes, namely the posession of a peptidoglycan wall. which neither Archaea or Eukaryotes posess. to my knowledge there are no archaea with walls, and Eukaryotic cell walls are made of other chemicals. to detail the differences between Archaea and Bacteria, the cell membranes are made of different chemicals, and also the transcription and translation mechanisms are different, and some archaea have different codon sequences, which are shared with Eukaryotic organelles, suggesting that Eukaryotes have inherited partially from Archaea, and partially from Bacteria (Margulis 1970). So even though our ancestors may have been defined today as prkaryotic, or at least to borrow Woese, progenote, we are not bacteria on the principle that some of our ancestors weren't either. To further the argument a little more, it is well known that much of our genetic material is provided by viruses, which are none of the above.
Margulis, Lynn, (1970), Origin of Eukaryotic Cells, Yale University Press
Woese, Carl R.; Fox, George E. (1977). "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–5090.
__________________ MSci MSc ARCS DIC PhD..... yes, I am bragging.
Hopefully Jet won't mind, but I'll post his/her/its latest comment from the other thread here too
just wanted to add a bit more now I am thinking about it. First of all prokaryotes and eukaryotes refers principally to an internal description of the cell, rather than being actual domains of life, so we will stick to general taxonomy and split them properly into bacteria, eukaryotes, and archaea.
another issue is that the bacteria have a cell wall made of peptidoglycan. while some eukaryotes have a cell wall, none are made of peptidoglycan. Another of the major domains is the Archaea which have their own differences namels the transcription and translation mechanisms. now it is interesting to note that some of our organelles have the same codon sequence as some archaea - i.e. the evidence is that these organelles are intracellularly symbiotic archaea. so given that archaea are not bacteria, well then neither are we since we are not in a monophyletic tree with the bacteria, since at least a part of us is derived from a different line.
I do see your point. But if we start breaking our conventions of taxonomy in this manner, then all plants and animals wouldn't be considered eukaryotes by the same logic, since animals/plants, while largely a product of an original eukaryotic stock, have separate genetic material from parallel branches of the tree of life.
Hopefully Jet won't mind, but I'll post his/her/its latest comment from the other thread here too
I do see your point. But if we start breaking our conventions of taxonomy in this manner, then all plants and animals wouldn't be considered eukaryotes by the same logic, since animals/plants, while largely a product of an original eukaryotic stock, have separate genetic material from parallel branches of the tree of life.
of course we are all eukaryotes - we all have the defining characteristic of eukaryotes.
__________________ MSci MSc ARCS DIC PhD..... yes, I am bragging.
First of all, I object to the claim that prokaryotes are a single domain, and here is my justification for doing so. The three domains in life are regarded as the bacteria, archaea and Eukaryotes (nucleated organisms), which are thought to have descended from an earlier progenote (Woese 1977). These three domains are separated by much more fundamental issues than internal structure, in the chemistry of the organisms.
The problem with trying to claim that we are prokaryotes based on the logic presented in the OP is that prokaryotes describes a specific characteristic that eukaryotes do not posess i.e. free DNA and lack of various intracellular structures. It would be akin to claiming that because our ancestors are tree - dwellers, then so are we. It is far more correct to define the domains as suggested, into these three categories, which have their own common group, to which we all belong.
To further the argument, it was claimed in the original thread that because of this, we are bacteria, and there is clear evidence against this. currently extant bacteria have a number of features that distinguish them from the other two domains, archaea and eukaryotes, namely the posession of a peptidoglycan wall. which neither Archaea or Eukaryotes posess. to my knowledge there are no archaea with walls, and Eukaryotic cell walls are made of other chemicals. to detail the differences between Archaea and Bacteria, the cell membranes are made of different chemicals, and also the transcription and translation mechanisms are different, and some archaea have different codon sequences, which are shared with Eukaryotic organelles, suggesting that Eukaryotes have inherited partially from Archaea, and partially from Bacteria (Margulis 1970). So even though our ancestors may have been defined today as prkaryotic, or at least to borrow Woese, progenote, we are not bacteria on the principle that some of our ancestors weren't either. To further the argument a little more, it is well known that much of our genetic material is provided by viruses, which are none of the above.
Margulis, Lynn, (1970), Origin of Eukaryotic Cells, Yale University Press
Woese, Carl R.; Fox, George E. (1977). "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–5090.
I do agree that the standard definition certainly makes us NOT prokaryotes for much the reason you described.
Actually, in conventional taxonomy that I've seen, Eukarya, Prokarya and Archaea are all held as having a common origin in "Biota" (Aron uses this standard). So Biota, or "living things," becomes the all-embracing way of identifying all life as having universal common ancestry.
But if our proposed evolution involves eukaryotes as being a subset of prokaryotes, then we'd still have to belong to prokarya. That the definition doesn't reflect this would indicate that the definition is based on an entirely different standard - though we both realize this, of course.
So, no, by presently accepted definition, we aren't prokaryotes. But I still don't get "why" - the thrust of your argument is that prokaryotes have a variety of unique features not shared by eukaryotes. But stegocephalian fish had a 2-chambered heart and fins, and we're still stegocephalian fish
Similarly, synapsid reptiles had metautostylic jaw attachment and a single temporal fenestra. Mammals have craniostylic jaw attachment and no temporal fenestra.
So are mammals still a subset of Synapsida? Many cladists hold it as such, as do I, even though many definitions of Synapsida include aspects that AREN'T present in some of its descendents (the mammals in particular).
To me, the logic of pro and eukaryotes mirrors this dilemma - though I don't see why the resolution wouldn't ultimately be the same.
of course we are all eukaryotes - we all have the defining characteristic of eukaryotes.
You're missing my point - those characteristics are based on the actual groupings within groupings of life. We're eukaryotes because we have a definition of eukaryotes which reflects all members of that taxon.
But we do have genetic material that is inherently NOT eukaryotic. As you suggested, we may have both prokaryotic and archaeic genetic material.
If you are making exceptions due to horizontal transfer, I'm suggesting that you're not applying that standard consistently across the board. Again - our definitions should reflect how life is actually grouped. Saying we're eukaryotes because we meet the definition of being a eukaryote is tautological.
I do agree that the standard definition certainly makes us NOT prokaryotes for much the reason you described.
Actually, in conventional taxonomy that I've seen, Eukarya, Prokarya and Archaea are all held as having a common origin in "Biota" (Aron uses this standard). So Biota, or "living things," becomes the all-embracing way of identifying all life as having universal common ancestry.
But if our proposed evolution involves eukaryotes as being a subset of prokaryotes, then we'd still have to belong to prokarya. That the definition doesn't reflect this would indicate that the definition is based on an entirely different standard - though we both realize this, of course.
So, no, by presently accepted definition, we aren't prokaryotes. But I still don't get "why" - the thrust of your argument is that prokaryotes have a variety of unique features not shared by eukaryotes. But stegocephalian fish had a 2-chambered heart and fins, and we're still stegocephalian fish
Similarly, synapsid reptiles had metautostylic jaw attachment and a single temporal fenestra. Mammals have craniostylic jaw attachment and no temporal fenestra.
So are mammals still a subset of Synapsida? Many cladists hold it as such, as do I, even though many definitions of Synapsida include aspects that AREN'T present in some of its descendents (the mammals in particular).
To me, the logic of pro and eukaryotes mirrors this dilemma - though I don't see why the resolution wouldn't ultimately be the same.
fair enough, I see your argument then.
__________________ MSci MSc ARCS DIC PhD..... yes, I am bragging.
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