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Author Topic:   Woese's progenote hypothesis
randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 31 of 194 (337782)
08-03-2006 5:26 PM
Reply to: Message 30 by Modulous
08-03-2006 5:16 PM


Re: war of the Woeses
Modulous, I mentioned the theoritical replicators in the OP. But isn't the idea that these replicators were subject to natural selection to a degree, as they competed for resources?
However, Woese is saying you can't have a replicating process that replicates things to a high degree of it's genotype because such evolutionary processes cannot account for the emergence of the 3 kingdoms, right?
So he posits a process which I think raises a significant problem with natural selection being involved at all since the genotype is not that connected to the phenotype. it seems more like the ole chance just happened to come up with all of the sudden the emergence of all 3 kingdoms indepedently. I mean how can you have natural selection work if the replicating process does not firmly connect genotype to the organism's features.
His claim is somewhat similar to the idea of the hopeful monster. For some reason, all of the sudden, we see an emergence of the 3 kingdoms. It's interesting to me how we see this sudden appearance aspect reflected in all of biota, the fossil record, etc,...but evos continue to hypothesize of gradualistic means of evolution which cannot and does not account for the life forms we see today.
Edited by randman, : No reason given.

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 Message 30 by Modulous, posted 08-03-2006 5:16 PM Modulous has replied

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 Message 32 by Modulous, posted 08-03-2006 6:10 PM randman has replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 32 of 194 (337790)
08-03-2006 6:10 PM
Reply to: Message 31 by randman
08-03-2006 5:26 PM


Re: war of the Woeses
Modulous, I mentioned the theoritical replicators in the OP. But isn't the idea that these replicators were subject to natural selection to a degree, as they competed for resources?
Basically yes.
However, Woese is saying you can't have a replicating process that replicates things to a high degree of it's genotype because such evolutionary processes cannot account for the emergence of the 3 kingdoms, right?
Sounds about right.
So he posits a process which I think raises a significant problem with natural selection being involved at all since the genotype is not that connected to the phenotype. it seems more like the ole chance just happened to come up with all of the sudden the emergence of all 3 kingdoms indepedently. I mean how can you have natural selection work if the replicating process does not firmly connect genotype to the organism's features.
If there is some connection with heredity, there is potential evolution (cumulative selection). The Devil is in the details, how much connection is there? what is the nature of that connection? etc etc.
His claim is somewhat similar to the idea of the hopeful monster. For some reason, all of the sudden, we see an emergence of the 3 kingdoms.
I might have missed it. What does Woese propose as the time scale of this 'sudden' emergence?

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 Message 31 by randman, posted 08-03-2006 5:26 PM randman has replied

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PaulK
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Posts: 17828
Joined: 01-10-2003
Member Rating: 2.5


Message 33 of 194 (337794)
08-03-2006 6:17 PM
Reply to: Message 22 by randman
08-03-2006 2:07 PM


Re: nothing taken out of context
Yes, Woese's claims are in thw OP, and it is quite clear that the "drastic and disruptive" changes refer only to evolving the phenotypes of two Kigndoms from another one.
In my opinion the changes in overall cell structure, organization, etc., re quired to change one of the three phenotypes into either of the others are too drastic and disruptive to have actually occurred.
(emphasis mine)
While mey researches have yet to find a clear answer on the status of the progenote hypothesis I have found statements that suggest that Woese has significantly modified his view and that the hypothesis is not widely accepted. Of course since you are the one pushing the paper it is your responsibility to show that it is not outdated, when even the author anticipated that it would be superceded some years ago.
As for the question of why it is futile to discuss things let me remind you that in a previous encounter you tried to argue that an essay that explicitly stated that universal common descent should not be considered a fact really claimed that univewrsal common descent WAS a fact. And that you used such rational arguments as quoting another article with a different author that happened to be on the same site. Or the argument that you had used the quote from the other essay earlier in the thread. Neither of which are even relevant, let alone adequate to override an explicit statement within the essay under discussion. And you accused me of not answering your points then, too. Even though I had. You, on the other hand never offered any reason whe we should disregard the explicit statement in the text, even though it was quoted for you more than once.
Edited by PaulK, : Add emphasis to quotei

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 Message 22 by randman, posted 08-03-2006 2:07 PM randman has replied

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ReverendDG
Member (Idle past 4141 days)
Posts: 1119
From: Topeka,kansas
Joined: 06-06-2005


Message 34 of 194 (337824)
08-03-2006 8:48 PM
Reply to: Message 7 by randman
08-03-2006 2:39 AM


Re: huh?
I am not attacking his paper but dealing with the facts he raised. You seem to want to avoid those facts.
what facts? the ones that he answers HIMSELF in the paper?, you are making a mountain out of a mole hill, if you read the paper he clarifies what he means without problems, other than you nitpicking quotes to make it look like he doesn't
Then why does he propose a progenote? I am not misrepresenting him at all here. You seem to not understand that what he proposes is that that there is no way at all for the universal ancestor to be a creature that reproduces like the creatures that descended from it. The gist of his paper is certainly not that this theoritical common ancestor simply was a mix of all 3 kingdoms, and in fact, the gist of the paper is the exact opposite in proposing a progenote!
i guess my eyes jumped over the last bit, must have been tired when i read it, but i still don't see where he said its a problem, you only quote part of what he said, and it seems that you have a problem with the idea of progenotes not him
I don't think that is possible considering your earlier misreading of his claims. Do you realize that a progenote is by definition a creature that lacks "precise linkage" as he says between phenotype and genotype? Isn't it obvious then why natural selection is an issue?
no, you don't seem to understand what he is saying at all, when he says "precise linkage" between phenotype and genotype, that the replication of gentics is not very developed in comparision to later life, this has very little to do with NS, this has to do with mutation and gentic make up
Rev, to be frank with you, your comments are just ignorant. Read the OP again carefully and pay attention this time. Woese raises a problem and offers a solution. You seem to be denying several things, that he raises a problem and solution and that there is a problem or solution, and so your entire post is wholly without any substantive comment whatsoever.
i guess when all you have is to ad-hom me for pointing out that you are reading selectively..
now you are making claims that i never did, your quotes that i challeged only show the problem and not the solution he came up with, maybe if you were more honest about it, you could read my post without jumping to conclutions.
i deny nothing. i said, that you are making him out to claiming this is a problem for NS and the ToE, you just continue to conflate his research and hypothosis as somehow being damaging to the ToE
being that this is fairly old by todays standards, i think we can find a lot more about this now
Edited by ReverendDG, : No reason given.

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Lithodid-Man
Member (Idle past 2961 days)
Posts: 504
From: Juneau, Alaska, USA
Joined: 03-22-2004


Message 35 of 194 (337843)
08-04-2006 12:29 AM
Reply to: Message 29 by randman
08-03-2006 5:11 PM


Re: Let me try to clarify....
Randman writes:
The molecular clock angle is interesting because it does suggest that the 3 kingdoms could not have arisen via present processes we observe today
This is essentially the gist of Woese's argument for a progenote. It would be better to state ... "via processes known in the mid 1980's" as I know there have been some advances since then. As I mentioned before, I have a few refs on ILL, they might have some more recent info.
Just to put my two cents in, I don't see how the progenote concept, as Woese defines, contains any explanatory power to the origin of the urkingdoms. I mean by definition (if you accept abiogenesis) something called a progenote had to have existed, but it doesn't explain very much about subsequent division of life. I agree with Rand on this, we should exhaust possibilities within what we do know before appealing to a hypothetical unknown, if that makes sense. Science is not served by putting forth unknowables as the explanation
I spoke briefly last week with a geneticist about the Woese paper (not about this aspect) and she commented that the paper was written before alot of new higher-rank taxonomy had been sorted out although it is generally still the same. One difference is that the hypothesis of multiple origins has pretty much died, as more genes are mapped we find too many similarities in too many places to be coincidence or even gene transfer. So if we accept abiogenesis, the ToE, and not the progenote we cannot consider multiple origin as a tenable hypothesis.
It is my suspicion that the issue lies (or formerly so) in our inability to see the whole picture. We are looking at three ancient lineages that seem very far apart. In all probability the differences wouldn't seem so great if we could look at a genetic sample from 3.5 bya.

Doctor Bashir: "Of all the stories you told me, which were true and which weren't?"
Elim Garak: "My dear Doctor, they're all true"
Doctor Bashir: "Even the lies?"
Elim Garak: "Especially the lies"

This message is a reply to:
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randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 36 of 194 (338027)
08-04-2006 10:47 PM
Reply to: Message 32 by Modulous
08-03-2006 6:10 PM


Re: war of the Woeses
I might have missed it. What does Woese propose as the time scale of this 'sudden' emergence?
Modulous, the concept of sudden emergence is not a time-scale issue, but the fact we cannot see the preceding, theoritical ancestor. Woese takes this a step further and says that current evolutionary paradigms, being based on gradualism due to creatures being genotes, cannot account for the emergence of the 3 kingdoms.
Now, have we ever heard of reasoning along these lines before?
Basically, the logic is pretty simple. The differences between the 3 kingdoms are far greater than the differences within the 3 kingdoms and yet they have been evolving far longer than the period between the hypothetical common ancestor and the emergence of the 3 kingdoms. Basically, all we observe is microevolution (if I can just put this in my own words), and though evos like to extrapolate microevolution as a process that can account for all of evolution, the truth is it cannot, and Woese recognizes that. So he proposes a radically different sort of evolution based on a hypothetical creature, a progenote.
It's actually quite an ingenious argument, a good save in the sense that the argument that evolution itself had to evolved sounds reasonable. However, it is not based on observation of facts and alternative explanations such as there being no common ancestor in the first place are just as strong an argument or stronger, but Woese at least attempts to honestly grapple with a real problem within the Theory of Evolution.
Edited by randman, : No reason given.

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 Message 39 by Jazzns, posted 08-05-2006 1:09 AM randman has replied

  
randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 37 of 194 (338028)
08-04-2006 10:48 PM
Reply to: Message 33 by PaulK
08-03-2006 6:17 PM


Re: nothing taken out of context
Yes, Woese's claims are in thw OP, and it is quite clear that the "drastic and disruptive" changes refer only to evolving the phenotypes of two Kigndoms from another one.
PaulK, you are still misreading what Woese is saying. Maybe you would accept it more from Lithidid-Man?
Have you read his posts? Woese is saying gradualistic evolutionary scenarios cannot account for the emergence of the 3 kingdoms. He's not just saying that one kingdom could not have evolved into the other 2, but that what we observe as evolution today, being based on all creatures being genotes, cannot account for their appearance, period. That's why he proposes a radically different type of evolution took place with a radically different sort of organism.
You seem to want to avoid recognizing that, which is the crux of what the paper is about.

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 Message 33 by PaulK, posted 08-03-2006 6:17 PM PaulK has replied

Replies to this message:
 Message 42 by PaulK, posted 08-05-2006 4:23 AM randman has replied

  
randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 38 of 194 (338037)
08-04-2006 11:14 PM
Reply to: Message 35 by Lithodid-Man
08-04-2006 12:29 AM


Re: Let me try to clarify....
One difference is that the hypothesis of multiple origins has pretty much died, as more genes are mapped we find too many similarities in too many places to be coincidence or even gene transfer.
This is one thing that doesn't make sense to me. Why conclude a common ancestor? I mean so what if similar genes are found. These genes are suppossed to have evolved from non-existence in the first place, right? Or they are the product of a Creator, right?
Either way or both ways, what all theories have is a common design and force bringing life into being and so since there is a common design and force no matter how it happened, there is no reason not to expect multiple origins not to produce the same genes.
The reason is that the properties of chemistry underlying genes is the same. If these properties, and this a massive and huge IF, but if as evos claim, these properties can somehow evolve into life, then these properties serve as a common design that life arises from, and so it would not be surprising to see the same designs genetically appear despite not sharing a common, living ancestor. They share the common ancestor of the properties of chemistry, if and I stress if the non-observed, unprovable and highly speculative theory of abiogenesis is true.
If abiogenesis isn't the way it happened, or if abiogenesis occured via a creative force (ID), then we have to consider the creative force or Intelligent Designer or whatever it is to be the commonality, and so asserting universal common descent is still a stretch. I will though admit that if ID is true, universal common descent is more plausible as this force or Person could overcome obstacles and "help" or cause the process and so common descent could be true.
But it seems to me the data suggests unaided universal common descent is unlikely, and that is why Woese comes up with a way to introduce a different sort of process than gradualistic evolution (so he can account for the data).

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Jazzns
Member (Idle past 3942 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 39 of 194 (338050)
08-05-2006 1:09 AM
Reply to: Message 36 by randman
08-04-2006 10:47 PM


Fact Check
Basically, the logic is pretty simple. The differences between the 3 kingdoms are far greater than the differences within the 3 kingdoms and yet they have been evolving far longer than the period between the hypothetical common ancestor and the emergence of the 3 kingdoms.
I am being lazy and just going to pose a question that I hope someone with more knowledge can answer.
What is the evidence for this statement that the 3 kingdoms have been evolving for longer than the period between the hypothetical common ancestor?
From my VERY rough and hazy memory from school many years back, I seem to recall that we have basic cellular life at 3.5GA and the division of the three kingdoms somewhere at 1.?GA. Even if the ? from the previous is large, doesn't that leave a heck of a long time for a variety of unicellular solutions to develop from some primitive forms?

Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

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 Message 36 by randman, posted 08-04-2006 10:47 PM randman has replied

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randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 40 of 194 (338056)
08-05-2006 2:29 AM
Reply to: Message 39 by Jazzns
08-05-2006 1:09 AM


Re: Fact Check
The division between bacteria and Archaea supposedly occured at 3.5 billion years ago; not that I think this is accurate mind you.

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randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 41 of 194 (338057)
08-05-2006 2:38 AM


a quick note
There seems to be a little confusion that somehow I am claiming the Progenote hypothesis is correct. Woese's paper was rudely thrust upon me as something I had to read and dissect amidst slurs by some that I had no understanding, blah, blah, blah.....all the usual idiocy. Well it turns out the paper was intesting in raising some facts that contradict or are problematic for evolutionary models.
So I started a new thread to discuss those facts. In no way am I defending Woese's hypothesis, but I think it was a good try.

  
PaulK
Member
Posts: 17828
Joined: 01-10-2003
Member Rating: 2.5


Message 42 of 194 (338065)
08-05-2006 4:23 AM
Reply to: Message 37 by randman
08-04-2006 10:48 PM


Re: nothing taken out of context
quote:
PaulK, you are still misreading what Woese is saying. Maybe you would accept it more from Lithidid-Man?
Not at all. The phrase "drastic and disruptive" occurs in relation to deriving two of the Kingdoms from a third, as I have shown. It appears nowhere else in the text quoted in the OP. Thus to use it in reference to anything else - as you did - is to take it out of context. QED.
quote:
Maybe you would accept it more from Lithidid-Man?
As you recognised early on, the point under issue is Woese's reasons for proposing a progenote. You asserted in the OP it was because "drastic and disruptive" changes would be required in more conventional scenarios (taking Woese's words out of context). Lithodid-man says that Woeses reasons for proposing a progenote lie in the molecular clock data Message 24, Message 35. Since you tell me to accept his posts - where he clearly disagees with you - citing molecular clock data instead - you are apparently admitting that you were in error.
Thus it seems that I was correct in pointing out that you had taken Woese's words out of context and as a result misrepresented his argument.

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RickJB
Member (Idle past 5021 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 43 of 194 (338072)
08-05-2006 7:19 AM
Reply to: Message 38 by randman
08-04-2006 11:14 PM


Re: Let me try to clarify....
randman writes:
If abiogenesis isn't the way it happened, or if abiogenesis occured via a creative force (ID), then we have to consider the creative force or Intelligent Designer or whatever it is to be the commonality,
There's no evidence for ID. If there's no evidence for ID why must it be considered?
randman writes:
But it seems to me the data suggests unaided universal common descent is unlikely
That is categorically NOT what Woese was saying. His assertion was that our current understanding of common descent is incomplete. Given the wealth of evidence we have in support of evolution common descent itself is not being questioned.
randman writes:
I will though admit that if ID is true, universal common descent is more plausible as this force or Person could overcome obstacles and "help" or cause the process and so common descent could be true.
How is it more plausible? Given that evolution has evidence it is far more implausible to assume the existence of a "designer" for which there is no evidence!
randman writes:
..and that is why Woese comes up with a way to introduce a different sort of process than gradualistic evolution (so he can account for the data).
No, he was attempting to expand on the ToE. That's science at work.
But I am interested in your arguments here, Randman. You seem to be suggesting that God intervened only in the earliest stages of evolution and that established mechanisms continued from there.
Are you proposing some form of theistic evolution, or do you reject the ToE in its entirity?
Edited by RickJB, : No reason given.
Edited by RickJB, : No reason given.
Edited by RickJB, : No reason given.

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Jazzns
Member (Idle past 3942 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 44 of 194 (338074)
08-05-2006 7:49 AM
Reply to: Message 40 by randman
08-05-2006 2:29 AM


Re: Fact Check
I guess I am just skeptical of that so I would like to see some reference. Really all 3 kingdoms are represented at 3.5GA?
I had the understanding that the evidence for life at 3.5GA was not specific enough to give us that kind of knowledge. If no experts chime in I'll see if I can look into this more later.

Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

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 Message 40 by randman, posted 08-05-2006 2:29 AM randman has replied

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randman 
Suspended Member (Idle past 4929 days)
Posts: 6367
Joined: 05-26-2005


Message 45 of 194 (338110)
08-05-2006 3:39 PM
Reply to: Message 44 by Jazzns
08-05-2006 7:49 AM


Re: Fact Check
I really don't know if all 3 are considered present, but that the split between 2 of them supposedly took place. It shouldn't be hard for you to look that up.

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