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Author Topic:   Woese's progenote hypothesis
Hyroglyphx
Inactive Member


Message 181 of 194 (339785)
08-13-2006 12:08 PM
Reply to: Message 177 by ramoss
08-12-2006 6:41 PM


Re: Multiple abiogenetic events
What you seem to not understand is that what the Miller/Ulrey experiment was trying to do. They were trying to show that complex organic chemicals can occur naturally, without life being present.Not only did they succeed, but we have refined the experiments for 50 years after their initial experiment. You are acting as if the Miller/Ulrey experiment was the beinging and ending of that line of inquiry.. it isn't.
The sole purpose of the inquiry was to solve the seemingly insoluble in purely materialistic terms. Consider what other applicable purpose it could have possibly served? And to be sure that the study was out of morbid interest to supplant the need and role of an Intelligence beyond us through some capricious force:
http://www.chem.duke.edu/...uise_chem/Exobiology/miller.html
Here was the problem with the experiment. The entire premise of the inquiry was to prove that life could have originated at random via a few simple compounds in a prebiotic soup, of sorts. (Pay no mind where even the simple chemicals came from). The claim was that miller had succesfully synethized proteins, such as adenine and guanine, but that he failed to produce cytosine and thymine. What's the first problem? Neither of those four bases are even proteins. Those are the four base pairs of a DNA molecule. So what did Miller actually produce and how did he produce it? Miller took what he thought must have been earth's early conditions, which in itself, is pure, unadulterated conjecture. He assumed that the earth's atmosphere was composed of very high concentrations of methane, ammonia, hydrogen, etc. From this volatile mixture, he used a spark ignition in attempt to make a combination that would allow life to come from non-life. What Dr. Miller atually created ws 85% tar, 3% carboxylic acid, and 12% non-living amino acids.
What does it take to arrive at just one protein? It takes 20 specific amino acids, placed in sequential order just to produce one protein. This means that Miller just took a wild guess as to what earth's atmosphere was actually comprised of and assumed that his pristine laboratory must have resembled those conditions. I mean, with his mixture, we could assume that a dirty diaper is a breeding ground for a prebiotic mixture, not just the propagation of bacteria. But perhaps my wording of failure was a bit execessive. It was a success on one level. Where as Louis Pastuer was officially credited with demonstrably proving that abiogenesis is impossible, perhaps it was Miller that sealed the deal once and for all. In those regards, the experiment was a success.

“If chance be the father of all flesh then disaster is his rainbow in the sky. And when you hear of, state of emergencies, sniper kills ten, youths go looting, bomb blasts school, it is but the sound of man worshipping his maker” -Steve Turner

This message is a reply to:
 Message 177 by ramoss, posted 08-12-2006 6:41 PM ramoss has not replied

Replies to this message:
 Message 182 by crashfrog, posted 08-13-2006 12:58 PM Hyroglyphx has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 182 of 194 (339792)
08-13-2006 12:58 PM
Reply to: Message 181 by Hyroglyphx
08-13-2006 12:08 PM


Re: Multiple abiogenetic events
And to be sure that the study was out of morbid interest to supplant the need and role of an Intelligence beyond us through some capricious force:
Oh, for God's sake. Both Miller and Urey were almost certainly theists. What possible interest would they have in trying to disprove the god of both their religions?
You need to get over these juvenile atheist conspiracy theories. Christians and other theists are overwhelmingly involved in research in evolutionary biology and biochemistry. The idea that all this science is just an atheist plot to disprove God is idiotic.
The entire premise of the inquiry was to prove that life could have originated at random via a few simple compounds in a prebiotic soup, of sorts.
Absolutely 100% false, as you've been repeatedly told. The purpose of the experiment was to establish whether or not amino acids could form under specific inorganic conditions.
It was an absolute success, of course. It was never, ever intended to prove the inorganic origin of life all by itself. How could you do that with a single experiment that didn't actually result in anything that was alive?
When you rebut a claim that your opponent didn't make, that you just made up yourself, that's called "arguing a stawman." That's exactly what you've done here. The purpose of the experiment was absolutely not what you describe, which is abundantly obvious if you actually look up the experiment you're talking about.
It takes 20 specific amino acids, placed in sequential order just to produce one protein.
Almost entirely incorrect. It's entirely possible to construct functional proteins from as few as 8 different aminos, and possibly even less. Certainly 20 aminos are employed by today's complex life, but there's no reason that all 20 are required right from the beginning.

This message is a reply to:
 Message 181 by Hyroglyphx, posted 08-13-2006 12:08 PM Hyroglyphx has replied

Replies to this message:
 Message 183 by Hyroglyphx, posted 08-13-2006 1:48 PM crashfrog has replied

  
Hyroglyphx
Inactive Member


Message 183 of 194 (339798)
08-13-2006 1:48 PM
Reply to: Message 182 by crashfrog
08-13-2006 12:58 PM


Re: Multiple abiogenetic events
Oh, for God's sake. Both Miller and Urey were almost certainly theists. What possible interest would they have in trying to disprove the god of both their religions?
Almost certainly theists? How have you deduced that from that their studies? What purpose does it serve to figure out how life could have originated at random and also believe in a Creator. A Creator needs 'create' in order to be a Creator. I think you're bright enough to realize that.
You need to get over these juvenile atheist conspiracy theories. Christians and other theists are overwhelmingly involved in research in evolutionary biology and biochemistry. The idea that all this science is just an atheist plot to disprove God is idiotic.
Crash, what other premise did it serve? What medicinal value is there in their study? What philanthropy could possibly have derived from the experiment? You claim that I'm spewing some conspiratorial rant but the premsie is quite clear. You tell me what purpose it served and we'll go from there.
Absolutely 100% false, as you've been repeatedly told. The purpose of the experiment was to establish whether or not amino acids could form under specific inorganic conditions.
LOL! Yeah, to show that life could have originated at random. Everyone knows this except you. Here's an interview with Miller. As you'll clearly see, he is defending the position that the inquiry is in support of abiogenesis. Closing your eyes won't make the monster disappear.
Just a moment...
When you rebut a claim that your opponent didn't make, that you just made up yourself, that's called "arguing a stawman." That's exactly what you've done here. The purpose of the experiment was absolutely not what you describe, which is abundantly obvious if you actually look up the experiment you're talking about.
Then tell me what purpose it served and why? Even in light of overwhelming evidence to the contrary.
It takes 20 specific amino acids, placed in sequential order just to produce one protein.
Almost entirely incorrect. It's entirely possible to construct functional proteins from as few as 8 different aminos, and possibly even less. Certainly 20 aminos are employed by today's complex life, but there's no reason that all 20 are required right from the beginning.
8 aminos? Then why do we see across the board with all organisms containing 20 amino's per protein, per molecule? Show me functional proteins with as little as 8 amino's , which amino's are they, and how have you come to such a radical conclusion?

“If chance be the father of all flesh then disaster is his rainbow in the sky. And when you hear of, state of emergencies, sniper kills ten, youths go looting, bomb blasts school, it is but the sound of man worshipping his maker” -Steve Turner

This message is a reply to:
 Message 182 by crashfrog, posted 08-13-2006 12:58 PM crashfrog has replied

Replies to this message:
 Message 184 by NosyNed, posted 08-13-2006 1:52 PM Hyroglyphx has not replied
 Message 185 by crashfrog, posted 08-13-2006 3:41 PM Hyroglyphx has not replied
 Message 186 by RickJB, posted 08-14-2006 3:52 AM Hyroglyphx has not replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 184 of 194 (339801)
08-13-2006 1:52 PM
Reply to: Message 183 by Hyroglyphx
08-13-2006 1:48 PM


To learn
Crash, what other premise did it serve?
To learn. Some people actually get off on learning new things and unwrapping the easter eggs buried in our universe.
Perhaps they were buried by your god; perhaps that's just the nature of the universe. We are still interested in learning whatever the ultimate cause of it all is. It has been demonstrated to you that theists and non can all have this desire to solve the riddles.
ABE
Another thing you can't seem to grasp is that many non-theists just don't give a moments thought to god in any given day. They do not care one wee little bit about disproving you ideas. I have known some who are researchers, both believing and not, and theological questions enter their minds very, very rarely.
It may be something central to your thinking but, understand this: most just don't care! Not a bit, zip, nada. It is only when forced upon them that they bother. Leave them alone and they will leave you alone. Do not start a reason and fact war when you are unarmed.
There is, on the part of some, a desire to show you to be wrong. Most just don't care. Amongst researchers those who give a darn are even rarer; they don't have time.
Edited by NosyNed, : Add an additional thought

This message is a reply to:
 Message 183 by Hyroglyphx, posted 08-13-2006 1:48 PM Hyroglyphx has not replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 185 of 194 (339831)
08-13-2006 3:41 PM
Reply to: Message 183 by Hyroglyphx
08-13-2006 1:48 PM


Re: Multiple abiogenetic events
What purpose does it serve to figure out how life could have originated at random and also believe in a Creator.
You'd have to ask them. But you'd have to be pretty ignorant of the vast scope of religious experience to assume that anybody who doesn't believe just like you is an atheist.
Crash, what other premise did it serve?
The exact premise that has explained to you. Did you not understand, or what? The purpose of the Miller/Urey research has been amply repeated to you, in several posts. Did we use too many large words, or what? Or do you simply not believe us?
Yeah, to show that life could have originated at random.
How would it do that?
As you'll clearly see, he is defending the position that the inquiry is in support of abiogenesis.
Of course the Miller/Urey experiments support abiogenesis. That's not what I'm saying at all.
What I'm saying is that, contrary to your repeated assertion, the purpose of the Miller/Urey experiment was not to single-handedly prove abiogenesis, so pointing out that it doesn't do that is irrelevant. Of course the experiment doesn't do something it wasn't intended to do.
It does do what it was intended to do - substantiate the inorganic origin of organic molecules. In that, it was a total success, and absolutely nothing that you've posted changes that.
Then tell me what purpose it served and why?
I've explained the purpose - to demonstrate that organic amino acids can arise through the sort of inorganic chemistry operating on the early Earth.
8 aminos? Then why do we see across the board with all organisms containing 20 amino's per protein, per molecule?
We don't see that, and you're clearly not very familiar with what we're talking about, because the majority of proteins are much, much longer than "20 amino acids per protein." Typically proteins are formed from hundreds of amino acids - actually just a part of the amino acid called a "residue" - not just 20. Often they're very small indeed, however.
Not every protein has to have all 20 residues. For instance, glucagon, a 29-residue protein, only has 17 different residues.
And why wouldn't it? Even the 20 amino acids employed by living things on Earth represent only a small fraction of all the known amino acids. There are hundreds upon hundreds of such amino acids. Living things even today use only a very small number of them. There's no reason to believe that that number couldn't have been even smaller in the past.
how have you come to such a radical conclusion?
I opened a textbook? I took a class?
In other words, I did exactly what you have never bothered to do - I studied the subject before making grand pronouncements about it.
Edited by crashfrog, : No reason given.

This message is a reply to:
 Message 183 by Hyroglyphx, posted 08-13-2006 1:48 PM Hyroglyphx has not replied

  
RickJB
Member (Idle past 4990 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 186 of 194 (339925)
08-14-2006 3:52 AM
Reply to: Message 183 by Hyroglyphx
08-13-2006 1:48 PM


Re: Multiple abiogenetic events
nemesis writes:
What purpose does it serve to figure out how life could have originated at random and also believe in a Creator. A Creator needs 'create' in order to be a Creator. I think you're bright enough to realize that.
How about using your imagination?
Who is is more powerful, a creator who sets the processes of an entire universe in motion, or one who has to create everything individually?
There's an entire universe out there that needed "creating"! For all anyone knows a Big Bang type event could have been God's single act of creation from which all else followed.
As far as I'm concerned, the God imagined by scientific theists is infinitely more compelling (and far less parochial) than the God imagined by anti-science literalists.
Edited by RickJB, : No reason given.

This message is a reply to:
 Message 183 by Hyroglyphx, posted 08-13-2006 1:48 PM Hyroglyphx has not replied

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


Message 187 of 194 (340430)
08-16-2006 4:56 AM
Reply to: Message 80 by randman
08-07-2006 9:17 PM


A Woese by any other name
how natural selection works if the phenotype is not precisely linked to the genotype.
It works fine at the moment and phenotype is not precisely linked to the genotype.
Incidentally, you didn't entirely respond to my Message 30. Woese has proposed nothing that is not consensus as far as the grand scheme of common ancestry goes. As far as the idea goes there had to be a time when the early replicators did things very differently than they do now. Woese proposes that the urkingdoms are the line beyond which things start happening differently, and gives a rather interesting reason why he proposes it.
Natural selection should work if there is any link between phenotype and genotype. The tighter the connection, the more 'useful' the selection is.

This message is a reply to:
 Message 80 by randman, posted 08-07-2006 9:17 PM randman has replied

Replies to this message:
 Message 188 by randman, posted 08-16-2006 6:33 PM Modulous has replied
 Message 189 by Brad McFall, posted 08-16-2006 7:06 PM Modulous has not replied

  
randman 
Suspended Member (Idle past 4898 days)
Posts: 6367
Joined: 05-26-2005


Message 188 of 194 (340594)
08-16-2006 6:33 PM
Reply to: Message 187 by Modulous
08-16-2006 4:56 AM


Re: A Woese by any other name
Seems to me you are advancing a semantics-based argument. Woese definitely proposes a non-vertical evolutionary process (you may want to read WK's comments), and so natural selection would presumably work in a semi-Lamarckian fashion with advantageous traits passed horizontally, and so though the organism's offspring wouldn't necessarily be advantaged, the trait would within the community as a whole.
As far as your comments, the thread is fairly narrowly defined. Woese proposes a hypothetical creature and process, non-observed, in order to counter specific problems he feels are insurmountable any other way.
Do you have a comment on the topic at hand or not?

This message is a reply to:
 Message 187 by Modulous, posted 08-16-2006 4:56 AM Modulous has replied

Replies to this message:
 Message 190 by Modulous, posted 08-17-2006 4:09 AM randman has not replied

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


Message 189 of 194 (340618)
08-16-2006 7:06 PM
Reply to: Message 187 by Modulous
08-16-2006 4:56 AM


Re: A Woese by any other name.."WIlliams"?
Making the argument that the phenotype and the genotype are precisely linked or linkABLE is perhaps a more tortuous route in the sense I rather than Gould intended (chapter "Species as Individuals in the Herierchical Theory of Selection" in Structure ofEvolutionaryTHeory Page648...)when he was determined to disACCount BOTH (actual footnote page 642) of Eldredrge's economic and Williams' "codical" dualized biologos hierarchies.
Woses' loosening of the aggregate geno-phenoTYPEs seems definiatively to me, even phonotically, to be due Williams' lapse nonmaterially of skiped organismic selectivity (as noted by Gould) but I also wish to deprecate in the "architect"(Gould's failure to extend the written design of form-making and translation in space to coherent vs perfect vs adherent" biologic of design" in a discontinuous morphospace) of complex organic adaptibility while an actual adaptation to be argued in group for was... contrary to Gould...
There MIGHT be room for the logical connections of Woses' and other breeds but I *suspect*(contra Wolfram as well) the organismic temporal and cyclical nautre of macrothermodynamics BETWEEN the mutation form and niche construction will rule out any dual hierarchy in biology and support Gould's position of a single hierarchy while also putting positive neobiological constraints on the CONCEPT of species selection.

This message is a reply to:
 Message 187 by Modulous, posted 08-16-2006 4:56 AM Modulous has not replied

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


Message 190 of 194 (340728)
08-17-2006 4:09 AM
Reply to: Message 188 by randman
08-16-2006 6:33 PM


Pedantic semantics
It seems that there is a major disconnect between my post and your reply which is indicative of some kind of communications problem. It could be you, me, or as is more commonly the case partially the fault of both parties. For example:
randman writes:
Woese definitely proposes a non-vertical evolutionary process (you may want to read WK's comments)
Is the kind of comment one might expect to see in reply to a post that says something like
quote:
Woese does not propose a non-vertical evolutionary process
which I certainly did not say. In Message 80 you questioned how natural selection can work if there is not precise linkage between phenotype and genotype:
randman writes:
Please show me where a progenote is and how it evolves, and how natural selection works if the phenotype is not precisely linked to the genotype.
I merely commented that natural selection works fine with modern organisms and in modern organisms the genotype is not precisely linked to the phenotype. I assume you agree that genotype and phenotype are not currently precisely linked and that natural selection works now.
randman writes:
As far as your comments, the thread is fairly narrowly defined. Woese proposes a hypothetical creature and process, non-observed, in order to counter specific problems he feels are insurmountable any other way.
This is precisely what I was discussing, so you must excuse me if I am confused as to how you missed this. Nevertheless accept my apologies if my posts were confusing or unclear. Let me try to rectify this. I am specifically discussing the 'hypothetical'/'non-observed' creature. Woese has done nothing inherently new in discussing these hypothetical entities.
That the early replicating entities were fundamentally different from modern and observed life is not a new concept - even at the time of this paper. That Woese proposes this entity is not the point, it's irrelevant! It's common sense that an entity fundamentally different from current life must have existed if the consensus opinion on common descent were to be true.
The only thing that makes Woese's ideas different is that he is specifying certain things - the temporal point before which life worked differently and one part of the nature of difference (less connect between genotype and phenotype).
Has my clarification succeeded? Are you now clearer on what I am trying to communicate to you?

This message is a reply to:
 Message 188 by randman, posted 08-16-2006 6:33 PM randman has not replied

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 191 of 194 (340915)
08-17-2006 8:11 PM
Reply to: Message 190 by Modulous
08-17-2006 4:09 AM


randman showcased
randman has been showcased (for now)
It certainly seems to me that most comments on this thread are arguing about the same things with different words.
Just my take.

This message is a reply to:
 Message 190 by Modulous, posted 08-17-2006 4:09 AM Modulous has not replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 192 of 194 (341792)
08-20-2006 8:03 PM


Woese's Tree of Life
In looking at the {evolution} entry on wikipedia I noticed a tree of life with the caption:
A hypothetical phylogenetic tree of all extant organisms, based on 16S rRNA gene sequence data, showing the evolutionary history of the three domains of life, bacteria, archaea and eukaryotes. Originally proposed by Carl Woese.
(color yellow and bold mine for empHASis)
When I clicked on the Carl Woese link it led me to
Carl Woese - Wikipedia
(where you can also see the tree)
Carl Richard Woese (born July 15, 1928) is an American microbiologist famous for defining the Archaea (a new domain or kingdom of life) in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1967, although not by that name. He was born in Syracuse, New York, on July 15, 1928. Woese is currently a professor of Microbiology at the University of Illinois at Urbana-Champaign.
Having defined Archaea as a new domain, Woese redrew the taxonomic tree. His system, based upon genetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, all incorporated within three domains: Bacteria, Archaea, and Eucarya. Archaea are neither Bacteria nor Eukaryotes. Looked at another way, they are Prokaryotes which are not Bacteria.
From this it appears that Woese clearly shows a common beginning to the three (for now) domains of life. I've circled the area of contention on this thread:

(click for larger version)
The only real question would appear to be whether he considers the beginning is {biotic\life} or {pre-biotic\material} and the best answer for that would be to ask Dr. Woese rather than make conjectures.
And in the end, this would still just be his opinion, so basing the validity of the whole theory of evolution or abiogenesis (or whatever Randman's point was) on this is just another faulty use of the argument from authority.
His opinion, no matter how well informed, is not necessarily the truth of what occurred. That's my take.
Enjoy.

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Replies to this message:
 Message 193 by Wounded King, posted 08-21-2006 2:51 AM RAZD has replied

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


Message 193 of 194 (341847)
08-21-2006 2:51 AM
Reply to: Message 192 by RAZD
08-20-2006 8:03 PM


Re: Woese's Tree of Life
The only real question would appear to be whether he considers the beginning is {biotic\life} or {pre-biotic\material} and the best answer for that would be to ask Dr. Woese rather than make conjectures.
I'm not sre where you get that this is the issue from. It is quite clear from Woese's published work that he considers the 'progenote' population from which the 3 kingdoms arose as biotic.
The great difference Woese proposes for the progenote is that there are no discrete genetic organisms as is the modern mode, instead there are lots of highly transmissable discrete genetic elements. While they may not constitute life as we know it they are certainly as alive as any of the pseudo biotic form such as viruses.
This horizontal transmission dominated community makes tracing discrete genetic lineages beyond a certain point problematic. In theory this could mask some sort of convergence from different abiotic origins, but if we accept Randman's idea that such multiple origins would all produce the same genetic system then the question is totally redundant anyway. Of course it makes Randman's idea completely useless, but there you go.
TTFN,
WK

This message is a reply to:
 Message 192 by RAZD, posted 08-20-2006 8:03 PM RAZD has replied

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 194 of 194 (345882)
09-01-2006 10:30 PM
Reply to: Message 193 by Wounded King
08-21-2006 2:51 AM


Woese things have happened
nearly slipped by this
I'm not sre where you get that this is the issue from. It is quite clear from Woese's published work that he considers the 'progenote' population from which the 3 kingdoms arose as biotic.
My lack of clarity\rushing the post. Coming here from the "definition of life" thread ...
While they may not constitute life as we know it they are certainly as alive as any of the pseudo biotic form such as viruses.
yeah, the issue (to me anyway) is whether this fits the definition of life, how Woese defines that, does that agree with other definitions or does his use of 'biotic' extend before 'life' - do virus types qualify, biotic but not life? or are they a fourth domain now? soon?
Thanks.

This message is a reply to:
 Message 193 by Wounded King, posted 08-21-2006 2:51 AM Wounded King has not replied

  
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