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Author Topic:   Woese's progenote hypothesis
RickJB
Member (Idle past 4990 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 136 of 194 (338672)
08-09-2006 5:48 AM
Reply to: Message 124 by Quetzal
08-08-2006 7:51 PM


Re: Request for Recap
quetzal writes:
So could someone explain what the issue is here? Thanks.
I asked that very question back in messge 81, if not earlier.

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 Message 124 by Quetzal, posted 08-08-2006 7:51 PM Quetzal has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 137 of 194 (338674)
08-09-2006 6:53 AM
Reply to: Message 83 by randman
08-08-2006 9:53 AM


Re: Woese's world
What do you make of it personally? Do you think, despite not observing this theoritical and Lamarckian evolutionary process, that Woese is right, or not?
I like woese's theory, it seems to quite elegantly provide a mechanism allowing for the development and optimisation of horizontal gene transmission in concert with refinements in the translational code.
I'm not 100% convinced that such a radical solution is neccessarily required to provide a basal common ancestor for the various cellular architectures, but Woese's approach may actually be the most parsimonious in some ways given that the common elements of the 3 kingdoms arguably aren't sufficient to provide a viable ancestral cell architecture.
If we accept Woese's argument that the genetic distances between the kingdoms is too great to fit in with a vertical lineage, even one with a moderate degree of HGT as in modern bacteria, then a period with HGT as a prime mover is probably required.
As Annafan suggests the communal period of cellular evolution is much akin to a genetic event horizon, with the lineages of many cellular systems being lost in the mix, there are however clearly a number of systems so basal to cellular function that they can be traced beyond what Woese would term the 'Darwinian transition'.
I don't think that our not having observed a progenote is particularly relevant to whether Woese is right or not. As others have pointed out we do observe the sort of Lamarckian evolution via HGT which Woese proposes to a limited extent through the swapping of plasmids in bacteria.
I certainly don't see any evidence at all to support the idea thay the 3 kingdoms didn't share a common ancestor, although such an ancestor may well have been a pre-cellular genetic community rather than what would be considered a single cell type today. In fact the genetic evidence does point to a common ancestor for a large number of cellular processes as woese's work on the aminoacyl-tRNA synthetases suggests (Woese et al., 2000).
TTFN,
WK
Edited by Wounded King, : No reason given.

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 Message 83 by randman, posted 08-08-2006 9:53 AM randman has replied

Replies to this message:
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Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 138 of 194 (338684)
08-09-2006 8:51 AM
Reply to: Message 128 by randman
08-09-2006 12:47 AM


Re: Request for Recap
Thanks for the summary.
That's one claim. It's certainly not his primary claim. He first claims that no common ancestor that reproduced and evolved as we see organisms do today could evolve all three.
Isn't that what I said?
quote:
Q writes:
Woese claimed that there was no way that one or more of the urkingdoms could have evolved from any of the others (the prokaryote to eukaryote idea, for instance).
That's his point. I think before deciding if his point has been superceded or is relevant, you ought to at least recognize what the point is.
I did recognize what Woese's point was. I was trying (and still am) to figure out what yours is.
WK has done a great job pointing out some key points in the paper. I agree that the progenote hypothesis provides an "elegant" solution to the question of precursers. On the other hand, I don't necessarily agree with Woese that there's something - a progenote - that necessarily has to be the ancestor of all three domains. More likely WK's precursor "community", where a single lineage is either indetectable or non-existent. On the other (other) hand, it is obvious that there was something that preceeded the rise of the three domains. However, the Rivera paper I cited clearly indicates that at least the earliest eukaryotes may have been chimerae. A hypothesis, btw, which supports Woese's idea that none of the three domains evolved into any of the others, but concurrently refutes his hypothesis about an identifiable "progenote", at least as far as eukaryotes go.
When we get down to the faint, fine line between the RNA world and the cellular world, there's very little hard evidence available, and speculation/data interpretation is relatively open. Given lateral gene transfer, genomic fusion, etc, at that level, and a much larger database today on genome sequences than Woese had available, we can even trace some specific inter-domain transfers. At the level Woese is talking about, these transfers relate to swapping operons and functional protein sequences among a group of non-genetic (as we understand the term) "organisms". These critters may not even be "life-as-we-know-it".
Be that as it may, the primary mechanisms of evolution - random changes and natural selection (especially purifying or stabilizing selection on functionality - see the Omlechenko paper I cited previously) would of necessity be operant. Thus you're going to have to be patient and explain why you think Woese's paper provides some kind of refutation or challenge to evolution. The ToE appears to be operating even at that pre-genetic level. Just not lineal descent, although even there we aren't sure what was going on down in the mud.
I still don't see what the fuss is about.
Edited by Quetzal, : eliminating "actually"s - three in a row was too much

This message is a reply to:
 Message 128 by randman, posted 08-09-2006 12:47 AM randman has replied

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Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 139 of 194 (338688)
08-09-2006 9:04 AM
Reply to: Message 129 by PaulK
08-09-2006 2:34 AM


Re: Request for Recap
The real issue is that randman claims that the paper is evidence against common ancestry of the three domains (or whatever you call them).
I think the Woese paper does in fact make the claim that there is no "universal common ancestor" when you get down to the pre-genetic line between an RNA world and the domains as we know them today. Obviously, that doesn't refute or even challenge the idea of common descent. It just means that the "last universal common ancestor" may in some sense be ancestors, plural. When we get down to that level, there's so much noise-to-signal that it is difficult to separate out what is going on from what isn't.
If rand is trying to make a case that descent with modification is bogus, he's going to need to come up with a different paper. That particular paper of Woese's doesn't provide the support he needs. It is, after all, a theoretical (read "speculative") scientific paper. Like all good speculative scientific papers, the hypothesis is based on solid data/observations (in this case, the differences in functional sequences between the domains). Beyond that, the paper simply discusses Woese's explanation for the data - his interpretation, if you will. Given his standing, it's obviously speculation that should be taken seriously. On the other hand, as you well know, just because Woese wrote it doesn't mean it's right...and parts have been shown to be to a degree incorrect by subsequent research. As is to be expected. Rand doesn't seem to get that part.
Edited by Quetzal, : Deleted another "actually" - bad habits are hard to break

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 Message 129 by PaulK, posted 08-09-2006 2:34 AM PaulK has replied

Replies to this message:
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Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 140 of 194 (338690)
08-09-2006 9:10 AM
Reply to: Message 133 by Annafan
08-09-2006 4:30 AM


Re: Request for Recap
hypothesis of gradual evolution from simple self-replicating molecules to the kind of life that we see now, will necessarilly go through a phase that can not be anything else but quite different from the current mechanisms.
As I tried to point out to rand, Woese doesn't postulate any new "mechanisms". LGT is an observed phenomena. We can even trace some of the inter-domain transfers back into the distant past. However, it's still all evolution by natural selection. There's really no better explanation for the differentiation, after all. It's just NS working on a different class of critters - but still working exactly the same as today. The ToE isn't affected at all, that I can see.
Nothing shocking there.
Indeed.
Edited by Quetzal, : murdered the final "actually"

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 141 of 194 (338693)
08-09-2006 9:22 AM
Reply to: Message 139 by Quetzal
08-09-2006 9:04 AM


Re: Request for Recap
Yes, Woese's authority applies equally to his interpretations of the data and the plausiblity of his proposed solution. Something randman doesn't seem to understand.
I believe that Woese is now in favour of the idea that the "common ancestor" was a community of replicators sharing genes. Certainly he proposes a good deal of HGT to explain why the archaeans and bacteria are not as distinct genetically as his ideas would suggest.
But a pool of common ancestors where we can't pick out THE ancestor is still common ancestry of a sort, and certainly not the independant origins preferred by randman. Woese's views call on known or plausible mechanisms to explain the similarities and the differences. If randman wishes to put his views on the same level then he needs to do the same, without relying on ad hoc assumptions (why, for instance, would an assumed designer create three lineages of single-celled life with the degree of shared similarities - and differences - that are observed ?)

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 142 of 194 (338753)
08-09-2006 5:22 PM
Reply to: Message 139 by Quetzal
08-09-2006 9:04 AM


Re: Request for Recap
quote:
It just means that the "last universal common ancestor" may in some sense be ancestors, plural.
I think this is probably what Will Provine meant when he said in passing to me, about a conversation he had with L. Margulis in Syracuse this past Spring, that he was personally not dissatisfied with NEVER knowing how the bacteria are properly to have been divided over time.
I thought that this was surprising (not in the context of evolutionary thought in general (which I would have had in the same breath with Richard Boyd on another occassion about species selection etc)) but only in reference to Will's comments about USING the chimp/human DNA differences/similarities against creationists without much of a segue in the same event as we/one might posit is available on EvC.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 143 of 194 (338918)
08-10-2006 10:42 AM
Reply to: Message 138 by Quetzal
08-09-2006 8:51 AM


Re: Request for Recap
There is a distinction between one of the kingdoms evolving into all three, and a precursor genote evolving into all three. Woese argues there could be no genote precursor because normal evolutionary processes are insufficient to explain the emergence of the 3 kingdoms. He also, as a subset of that argument, states that one kingdom could not evolve all three even though if there was just one kingdom, that could be explained by a genote precursor.
The relevance here is first is that the alternative explanation is that the 3 kingdoms may not have shared a common ancestor. A larger question, but probably beyond the scope of this thread is that this fits a pattern of the common ancestor for various taxa being absent. For example, we never see any living common ancestors, nor in the fossil record, and Woese has a problem with microevolutionary processes of evolution we observe today being sufficient to explain the emergence of the 3 kingdoms.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 144 of 194 (338919)
08-10-2006 10:44 AM
Reply to: Message 140 by Quetzal
08-09-2006 9:10 AM


Re: Request for Recap
However, it's still all evolution by natural selection.
\
It's not natural selection on vertical evolution, meaning natural selection on an organism itself, and so it's really not the same thing at all.
Of course, handwaiving this away is not unexpected from the evo side of things.
Edited by randman, : No reason given.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 145 of 194 (338922)
08-10-2006 10:56 AM
Reply to: Message 137 by Wounded King
08-09-2006 6:53 AM


Re: Woese's world
I certainly don't see any evidence at all to support the idea thay the 3 kingdoms didn't share a common ancestor, although such an ancestor may well have been a pre-cellular genetic community rather than what would be considered a single cell type today. In fact the genetic evidence does point to a common ancestor for a large number of cellular processes as woese's work on the aminoacyl-tRNA synthetases suggests (Woese et al., 2000).
Why would the "common ancestor" not just be the design properties within chemistry? Certainly, if the chemical properties of whatever suppossedly spontaneously evolved into life are indeed capable of that, wouldn't they necessarily exert a common influence by their physical properties?
Woese's approach may actually be the most parsimonious in some ways given that the common elements of the 3 kingdoms arguably aren't sufficient to provide a viable ancestral cell architecture.
If we accept Woese's argument that the genetic distances between the kingdoms is too great to fit in with a vertical lineage, even one with a moderate degree of HGT as in modern bacteria, then a period with HGT as a prime mover is probably required.
Or could the explanation simply be that there was more than one event of spontaneous generation of life?
I am not saying that I agree with abiogenesis, btw, but the adherence to the one-time only, or the one-time that made it only, doesn't seem very likely. if evolving into life is a property of chemistry, then we should expect it to happen often over vast periods of time.

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 Message 137 by Wounded King, posted 08-09-2006 6:53 AM Wounded King has replied

Replies to this message:
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kuresu
Member (Idle past 2513 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 146 of 194 (338926)
08-10-2006 11:10 AM
Reply to: Message 145 by randman
08-10-2006 10:56 AM


Re: Woese's world
what if our common ancestor, or ancestors, were the ones to make it, and all other attempts failed. keep in mind, the earth is large, a million plus years is a damn long time. it isn't too mind boggling to think that there could have been other successful attempts. just, our ancestors were the best.
after all, there still is survival of the fittest.
there may have been non-carbon based life, using heavier atoms. there imagining something similar might be possible of Titan, one of saturn's moons (if it's not titan, its the one with the volcanos and methane ocean). life using methane instead of water.
the only thing we know for sure is that there was no life at one point. and then, there was life. and we are the only living things left. we, as in all of us DNA, carbon based lifeforms, are all that's left.
oh, and just because Woese couldn't, or still can't, see how a genote could evolve into the three domains with vertical evolution does not make it so. he could be completely wrong. quetzal already mentioned the symbiosis theory (name right?) where eukaryotes were formed by the synthesis of a couple to several bacteria into one unicellular organism. that knocks out one kingdom. the other thing, is that as far as I know, we know the chemical pathways, the cell structure, etc of archaebacteria, uebacteria, and eukaryotes of today, and we're fairly certain of what they were millions of years ago. question is, when they first split, were bacteria and archaebacteria really that different? or has that difference come along? does he have any data for this? is their any new data as to this?

All a man's knowledge comes from his experiences

This message is a reply to:
 Message 145 by randman, posted 08-10-2006 10:56 AM randman has replied

Replies to this message:
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kuresu
Member (Idle past 2513 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 147 of 194 (338927)
08-10-2006 11:11 AM
Reply to: Message 144 by randman
08-10-2006 10:44 AM


Re: Request for Recap
like the handwaving Behe did just recently, in regards to a reconstructed (Hox1 ?) gene?

All a man's knowledge comes from his experiences

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 148 of 194 (338932)
08-10-2006 11:26 AM
Reply to: Message 146 by kuresu
08-10-2006 11:10 AM


Re: Woese's world
what if
What if God-did-it? Oh, your "what-if" just-so story is OK, but no on else's?
the only thing we know for sure is that there was no life at one point. and then, there was life.
We don't know that for sure. For all we know, life existed and the evidence from so long back just didn't remain.
after all, there still is survival of the fittest.
This ignores an interdependence aspect to life. Human beings may be more fit, for example, than cattle, but we keep them around for meat. The idea that one lineage would be squeezed out rather than both depending on the other is wholly unproven and illogical, and just more mythmaking on the evo-side of things.
The myth is that somehow, just be chance, a singular event occurred, and gave rise to life, which then competed with one another to evolve everything we soo today, totally via chance I might add. It's a myth, and never was nor ever has been validated by empirical data.
The whole idea of the singular event, or the singular event that somehow beat out all the rest is illogical. If within the properties of chemistry, there is the likelihood of evolving life, a big IF, then life would have evolved a bunch of times over such long periods of time, and if life evolved bunches of times, chances are that there would be considerable interdependence such that more than one lineage would survive, and if this magical story really happened, chances are since the real common ancestor would be the properties of chemistry, then we would expect to see all the various commonalities you guys insist can only be explained via one living ancestor species or group.

This message is a reply to:
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kuresu
Member (Idle past 2513 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 149 of 194 (338942)
08-10-2006 11:53 AM
Reply to: Message 148 by randman
08-10-2006 11:26 AM


Re: Woese's world
We don't know that for sure. For all we know, life existed and the evidence from so long back just didn't remain
so you disagree that at one point the universe didn't exist. you think it's always existed. what about earth, surely god did create it. and surely, he created it before he created life on earth, right? or have we all been misreading genesis.
What if God-did-it? Oh, your "what-if" just-so story is OK, but no on else's?
see, that's the problem. you play the what if game. why can't I propose my own what if? why is your what if about the chemicals explaining commonality right, and our what if about chance wrong?
see, you want us to all believe in your what if, whether or not it's creationism or ID (i'm not sure which you are, but my guess is former). you want us to have that taught in our schools as science. well, that's just one, and only one what if story. and there are plenty of other stories about creation, pretty much one for every religion on the planet.
playing the waht if game is dangerous. you have to back it up with evidence. evidence is, life isn't starting again and again today. but we do know that organic molecules can form on their own, given the right conditions. those conditions were met in hte atmoshpere of the early earth. you ask why can't life have started plenty of times. I gave you a possible scenario, which you reject as illogical. but let's deal with some facts here, okay.
A) there was, at one point, no life on earth
B) there was, at a later point, life on eath
C) organic molecules, such as amino acids and nucleic acids, can form given the proper condition.
D) the only life we know of is carbon based and uses DNA/RNA
E) we know that the conditions for the creation of organic molecules existed on the early earth for quite some time, easily a million years.
conclusion)at some point and time in earth's history, when hte conditions were right, life did get started. if life got started multiple times, our line of ancestry is the only one represented if other forms of life existed that did not use DNA/RNA (or the precursor forms that have been suggested) and were not carbon based. If these life forms did exist, that were not like us, they no longer exist as far as we can tell. if this is the case, we outcompeted them, or were more fit to live in the initial environment than they were.
the second possibility is that we are the only life form (carbon based, DNA/RNA, precursors) to have ever existed on this planet.
tell me randman, how is my conlcusion illogical, given the facts. it's no longer a mere what if story, it's a what if story with facts. can you say the same of genesis?
oh, one last thing.
Human beings may be more fit, for example, than cattle,
this comment betrays an ignorance as to what being fit entails. are cattle more fit than us? depends on the habitat, and their. cattle cannot do what we do--they can't build cities, develop technologies, nor are they as smart as us. but you know what, they are quite excellent at what they do. eating grass. their digestive system is much, much better at breaking down the grass, hay, that they eat, unlike our digestive system, which can't even break down cellulose. If we were to be a herd of grass eaters, those cows (cattle) would beat us out.
the suggestion I find illogical is that the properties of chemistry should be our common ancestor, especially since the comm ancestor idea is a biological one, and deals with evolution. last time I checked, it doens't really matter what caused the first life to appear, in terms of evolution and common ancestors. because, the common ancestor is defined, pretty much, as being that organism(s) that gave rise to the life we see today by the methods and processes of evolution.
notice the lack of chemistry?

All a man's knowledge comes from his experiences

This message is a reply to:
 Message 148 by randman, posted 08-10-2006 11:26 AM randman has replied

Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 150 of 194 (338949)
08-10-2006 12:04 PM
Reply to: Message 145 by randman
08-10-2006 10:56 AM


Multiple abiogenetic events
Why would the "common ancestor" not just be the design properties within chemistry?
Because there is more than one chemical solution to many of the functional structures which suggest a common ancestor.
If there were only one possible amino acid sequence for a particular protein or only one possible genetic code then you might have a case for their having arisen independently, but as it is the conservation of these elements when there are alternative possibilities argues for a common ancestor.
Or could the explanation simply be that there was more than one event of spontaneous generation of life?
This could be the case but it would not solve Woese's problem. If we were to accept multiple different abiogenetic events then to fit the progenote scenario or contribute to modern cells they would all need to have been part of the pre-genomic pre-vertical community. The level of commonality between all cells cannot be explained by 3 distinct instance of abiogenesis, even if we were to allow for arguments sake that distinct isolate abiogenetic events would give rise to the same basic genetic elements.
So while we might imagine that self replicating RNAs may arise more than once in isolation, or even go as far as to utilise DNA as a more stable genetic medium, there is no way we can go as far as allowing for the genetic code, the transcriptional machinery and many other conserved cellular features to be explained in this way.
if evolving into life is a property of chemistry, then we should expect it to happen often over vast periods of time.
This doesn't really follow, not without knowing the actual chemistries and circumstances required. This is yet another intuitive estimate of the probability of abiogenesis, only instead of the usual claim that it is too fantastically improbable ever to happen you are claiming that it is so probable that it should be happening all the time.
Human beings may be more fit, for example, than cattle, but we keep them around for meat. The idea that one lineage would be squeezed out rather than both depending on the other is wholly unproven and illogical, and just more mythmaking on the evo-side of things.
Since humans and cattle are not competing for a common ecological niche this seems like a rather weak argument, especially since man has wiped out so many species. Even if we allow interniche competition if we compare the number of species man maintains domestically with those he has had a hand in 'squeezing out' I think the weight of evidence comes doen heavily on the side of squeezing out.
TTFN,
WK

This message is a reply to:
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