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Topic: Pun, Schuldt, and Pun: The Three Domains of Life: A Challenge to the concept...
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posted 26. July 2002 12:15
[Editor's Note: This paper is being pre-published for discussion purposes and a revised version will appear later in the publication Origins & Design.]
The Three Domains of Life: A Challenge to the concept of the Universal Cellular Ancestor?
by Pattle.P.Pun, Stephen Schuldt, and Benjamin T. Pun
pattle.p.pun@wheaton.edu
ABSTRACT—With the discovery of the uniqueness of Archaebacteria in rRNA sequence and by comparative studies with well-characterized molecular systems, cell walls, lipid compositions and features of the transcriptional and translational machineries, the three domains of life, namely Archaea, Bacteria and Eukarya, has become the currently accepted paradigm in the field of molecular taxonomy. Sequence analyses based on functional proteins across the three domains also suggest each of the three domains as independent monophyletic lineage representing ribosomal, metabolic, biosynthetic proteins as well as the replicational, transcriptional and translational machineries. Current view suggests that the universal tree of life branched from the universal ancestor in separate lineages leading to Bacteria and Archaea, the latter then diverged into Eukarya. The search for the universal ancestor has led to postulating a universal communal gene pool (progenotes) in which lateral or horizontal gene transfer (HGT) played the most important role in diversification since the three domains of life are resistant to HGT after they have crystallized into cellular communities. This scenario challenges the concept of the Universal Cellular Ancestor and may be open to alternative views based on design.
To read the entire paper, please click here
[ 09. October 2002, 17:59: Message edited by: Moderator ]
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Frances
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posted 10. August 2002 22:25
Interesting paper but I fail to see the relevance of this paper to design. While the data may point to more than one universal ancestor, this is hardly a problem per se for evolution. Even Darwin envisioned the possibility of more than one ancestor.
Since I have yet to see how design can be limited in what it can and cannot do or explain I fear that this paper merely has pointed out that there may be multiple origins but that's not really something new or shocking. Others have done so before.
My question is: Does the data support common descent from _multiple_ ancestors and what impact would this have on evolution and intelligent design? And more importantly what does this paper have to contribute to intelligent design?
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Pattle P. Pun
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posted 12. August 2002 18:00
I am suggesting that concept of common descent implying the most parsimonious interpretation of a single universal cellular ancestor has to be reexamined. Natural selection cannot work on an acellular community of gene. One has to propose self organizational machine or other models based on emergence as I suggested in my paper. Then the idea of design as a "mind-correlated pattern" either as an algorithm or pruning framework can be proposed, instead of the current ideas of abiogenesis based on probability and selection.
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Art
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posted 12. August 2002 20:00
Pattle Pun stated: quote:
Natural selection cannot work on an acellular community of gene.
I do not agree with this comment. If one thinks about the simple pathway I describe in this thread as a sort of acellular pathway, one can readily see how selective pressures - in this case, rates of breakdown of one of the intermediates that approach their rates of utilization - can act to increase utilization to preserve or restore a measure of robustness in the system. If the persistence of the system depends on robust flux, then we have a state whereby natural selection can modify the catalysts for the intermediate steps.
I think it's useful to ask about the relevance of Darwinian mechanisms to pre-biotic models. But it is not appropriate, IMO, to ignore their relevance out-of-hand by declaring that they only act on cellular life as we know it.
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Frances
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posted 13. August 2002 01:00
Dear Sir,
I know what you are suggesting and this suggestion is not new. Even Darwin considered the possibility of multiple origins. In fact multitple origins do not seem to be a problem for evolution per se since evolution merely deals with what happened afterwards. But what I fail to understand is the somewhat ad hoc inclusion of 'intelligent design' in the paper. It seems to me an unnecessary after thought. But perhaps I am missing something here, is there a link to intelligent design? If so what form does this link take? Is it ICness, or is it more like Dembski's ID?
[ 13 August 2002, 01:01: Message edited by: Frances ]
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charlie d.
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posted 13. August 2002 10:23
I thought this was an OK paper as far as data analysis is concerned (though that is not my field), but the key statement
"However, the implication of polyphyletic origins of the three domains of life from a universal pool of progenotes seems to demand a mechanism beyond the realm in which Darwinian natural selection can operate (Doolittle, 2000; Woese, 1998, 2000)."
appears entirely unsubstantiated, either theoretically or empirically (none of the 3 references, as far as I can tell, support the authors' statement either).
In fact, natural selection is usually considered a necessary product of inaccurate self-replicating systems in replication-limiting environments, and the issue of pre-cellular natural selection has been addressed formally in a number of studies (most recently, to my knowledge, in Segre D, Ben-Eli D, Lancet D. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4112-7.).
It is somewhat suprising that the authors do not refer to any of these previous studies so relevant to their own. Personally, I think that for any reviewer/reader to be able to evaluate their conclusions, the authors should explicitly discuss why they assume natural selection would/could not act at the precellular stage of evolution.
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Pattle P. Pun
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posted 14. August 2002 12:19
3 observations:
I: By "Darwinian Natural Selection", most geneticists are referring to the classical definition based on population and molecular genetics: (Natural Selection in the Wild: by John A. Endler, Princeton Univ. Press, 1986, p. 4)
"Natural Selection can be defined as a process in which:
a. variation among individuals in some attribute or trait: variation;
b. a consistent relationship between that trait and mating ability, fertilizing ability, fertility, fecundity, and, or, survivorship: fitness differences;
c. a consistent relationship, for that trait, between parents and their offspring, which is at least partially independent of common environmental effects: inheritance;
Then:
1. the trait frequency distribution will differ among age classes or life-history stages, beyond that expected from ontogeny;
2. if the population is not at equilibrium, then the trait distribution of all offspring in the population will be predictably different from that of all parents, beyond that expected from conditions a and c alone.
Conditions a,b,and c are necessary and sufficient for the process of natural selection to occur, and these lead to deductions 1 and 2. As a result of this process, but not necessarily, the trait distribution may change in a predictable way over many generations. .....(Natural Selection) proceeds not for biological reasons by from the laws of probability; conditions a-c contain the only biological content"
In this strict sense, acellullar systems do not have sufficient biological content for Darwinian natural selection to act upon.
II. Carl R. Woese in his recent article "On the evolution of cells, Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 13, 8742-8747, June 25, 2002" essentially suggests Darwinian natural selection only occurs after the "Darwinian threshold" of cellular life has been achieved. See the abstract below:
"A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given."
III. Geneticist Gabriel Dover claims that there is a third force in evolution: ("Dear Mr. Darwin, Letters on the evolution of Life and Human Nature" Univ. of Calif. Press, 2000)
'Molecular Drive' beside natural selection and neutral drift.
Molecular drive is operationally distinct from Darwinian natural selection and neutral drift. According to Dover it explains biological phenomena, such as the 700 copies of a ribosomal RNA genes in the human genome and the origin of the 173 legs of the centipede, which natural selection and neutral drift alone cannot explain.
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Frances
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posted 14. August 2002 12:37
So evolution has more than a single mechanism? Hardly that surprising given the fact that genetic drift has been known for quite a while. So now we have to add horizontal gene transfer as well as a complicating factor. But how does all this help the case of Intelligent Design? To me the latter seems to be more a wishful after thought and not something that follows logically from the data.
As I have shown even Darwin addressed the possibility of multiple origins so common descent need not require a single common origin of life.
Could you perhaps explain to me the relevance of your paper to ID?
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Pattle P. Pun
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posted 15. August 2002 12:13
Dear Frances,
Although I do not have any concrete ideas on models based on design yet, the sequence data seem to lead us to examine other models than Darwinism. Dembski quoted a prominent biologist, a member of the National Academy of Science (whom he declined to name)who sees three main alternatives to biology: (1) Intelligent Design, (2) Darwinism, (3) some natural biological processes yet undiscovered. The models of Molecular Drive and Self Organization are not well understood and tested. Then the idea of design as a "mind-correlated pattern" either as an algorithm or pruning framework can also be proposed, i.e, some pre-existing patterns or "designs" are the raw-material of biological development. In other words, there are genuine "discontinuities" in nature. These ideas are valid scientific thoughts that can be further developed and tested. I am hoping others in ISCID or people such as the aforementioned scientists who are open-minded enough to examine the different ways of approaching the origins problem.
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charlie d.
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posted 16. August 2002 19:45
I still see no explanation of why natural selection should not be able to work at the pre-cellular level, nor discussions of previous work in the specific field.
The reference to Woese's "Darwinian threshold" is not really relevant: what he is arguing in the quoted passage is that Darwin's original view of natural selection, as working exclusively at the organismal level, could only start to operate in cellular organisms. However, the concept of selection at molecular level, such as genes and selfish DNA elements, is now, almost 150 years later, quite accepted.
The reference to Dover's molecular drive is also unclear to me. I can't say I have the concept firmly down (my impression is, few besides Dover do) but it seems to me that molecular drive refers specifically to the "lateral" spreading of certain features among members of a multisequence/multigene family, driven by their own molecular properties (for instance, a propensity to intragenic recombination, gene conversion, further duplication and such). Hardly the stuff that changes our outlook on the origin and history of life, and certainly not teleological or design-friendly in any significant way.
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Frances
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posted 17. August 2002 13:32
Dear Pattle,
It seems to me that your response suggests that ID remains a possibility when we do not understand the full details but that is trivially true since ID is not infered from positive evidence but through elimination of known and unknown natural processes.
Which seems to make the inclusion of the references to ID meaningless since as you mention there are no concrete ideas or models of design (yet?).
Which brings me back to my original observation that ID seemed to be an (unnecessary) after thought to a interesting paper.
Unless ID wants to quote any paper which finds results we do not yet understand as evidence of ID, it seems that ID should focus on a more positive approach to Intelligent Design. For instance a model, mechanism that would limit the explanatory power of ID to something less than 'we don't know yet'.
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Mike Gene
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posted 17. August 2002 14:23
Hi Pattle,
Your article notes:
One question that remains is whether lateral gene transfer is truly a major component of genome evolution. The examples of lateral gene transfer that are published in the literature often involve specific, isolated lineages, such as the occurrence of glutaminyl-tRNA synthetase in certain bacterial groups (Doolittle and Handy, 1998). In contrast to isolated incidents, rampant gene transfer should abolish our ability to recognize coherent evolutionary lineages.
I think this is a good point. It seems that most of the evidence for ancient lateral transfer indicates such transfer not only took place after archaea and eubacteria split, but after the two domains split into their respective major groupings. I kind of touched on this when many of us discussed Woese's latest PNAS paper on ARN:
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One reason why many might consider this article ID-friendly is because it is easy to view this thesis as a heroic attempt to give a teleological cause a non-teleological explanation.* But in doing so, Woese abandons cell biology. That is, the cause behind the last common ancestor of bacteria, archaea, and eukarya is not a cell being shaped by Darwinian evolution, but some misty entities quite unlike anything biology has ever studied. It's quite an extraordinary claim oddly lacking the "extraordinary evidence" that is supposed (so we are told) to come with such claims. If one is going to extrapolate such a weird non-teleological world, it becomes a little harder to be incredulous about extrapolating a teleological cause. And buried in Woese's claims is the lack of belief that a bacterial cell could evolve into a eukaryotic cell through Darwinian evolution. In fact, he even questions the need to invoke endosymbiosis, in light of his hypothesis (I can't find the passage, as I did not highlight it, but I'll look later).
There seems to be significant tension in Woese's thesis. His objective is to take various cell-dependent processes and imagine them to exist without cells in order to come back to explain the origin of cells. His cornerstone is HGT. But HGT is a cell-dependent process. Every mechanism of HGT entails not only the existence of the cell, but also some rather sophisticated machinery. There is no need to postulate HGT in a cell-independent fashion. In fact, there seems to be a certain degree of arbitrariness in asserting that life begin with three cell types crossing this 'Darwinian threshold' and its not clear why Woese's thesis doesn't collapse into something like Schwabe's thesis. For example, 1/5 genes from E. coli were acquired through HGT. 1/4 genes from Thermotoga appear to come from archaea. Some members of eubacteria, such as spirochetes, have V-ATPases instead in the more commonly found F-ATPases. One can make a circumstantial case that at some point, there is enough shared machinery to justify a monophyletic crossing of the 'Darwinian threshold,' but that threshold looks very fuzzy and assumption-dependent to me.
*My working hypothesis is that life was seeded as a heterogeneous pool of cells, each with the ability to cross-talk. I've explained the independent design reasoning for these features before. Woese's hypothesis looks like an attempt to explain such an origin from a non-teleological perspective.
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As for the notion that ID is irrelevant to Pattle's paper, I suppose it all comes back to what we expect from ID. Are we looking for proof of ID? Are we looking for something that only ID can explain? I suggest one tie-in comes from a thread where Jay and I discussed molecular examples of "convergence." Might these three cell types be the cellular equivalent of things Jay and I were talking about - too similar for chance, yet too different for common descent?
Then there is the really interesting question not even addressed by mainstream science - why three cell types? Why these three cell types? Is the answer, "stuff happens" or is there a deeper logic behind it all?
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Frances
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posted 17. August 2002 15:09
Mike:
quote:
As for the notion that ID is irrelevant to Pattle's paper, I suppose it all comes back to what we expect from ID. Are we looking for proof of ID? Are we looking for something that only ID can explain?
That's an excellent question but that requires us to understand what the explanatory powers of ID are. At the moment ID's "explanatory powers" seem to involve areas in which our understanding is lacking and since I would not consider our ignorance to have much explanatory power, I would suggest that in order for ID to have any explanatory power we need to for instance know more about the mechanisms, the designer(s), the motives etc. Without such what are the limitations of ID?
quote:
Then there is the really interesting question not even addressed by mainstream science - why three cell types? Why these three cell types? Is the answer, "stuff happens" or is there a deeper logic behind it all?
I am glad that Mike seems to realize that in order for us to determine ID we need to know the 'why' which requires us to know either motives or mechanisms.
Until ID grows beyond the idea of that which remains when we eliminate "chance", the usefulness of ID would seem to remain very limited.
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charlie d.
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posted 17. August 2002 15:30
quote:
As for the notion that ID is irrelevant to Pattle's paper, I suppose it all comes back to what we expect from ID. Are we looking for proof of ID? Are we looking for something that only ID can explain?
Mike, maybe you aren't, but Pun et al certainly are looking for (and claiming to have found) something Darwinian mechanisms cannot explain, and ID can: "... the implication of polyphyletic origins of the three domains of life from a universal pool of progenotes seems to demand a mechanism beyond the realm in which Darwinian natural selection can operate (Doolittle, 2000; Woese, 1998, 2000)."Asking them to justify their assertion, expressed in the context of a scientific paper, seems to be a minimal requirement, or isn't it?
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