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Author Topic:   Transition from chemistry to biology
DNAunion
Inactive Member


Message 10 of 415 (77433)
01-09-2004 7:39 PM
Reply to: Message 4 by sidelined
01-05-2004 9:39 PM


Wait a tick. The definition you guys are giving for abiogenesis also fits spontaneous generation, and didn't "you guys" give some "Creationist" a verbal pummeling a week or so ago for confusing the two?

[This message has been edited by DNAunion, 01-09-2004]


This message is a reply to:
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Replies to this message:
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DNAunion
Inactive Member


Message 14 of 415 (77441)
01-09-2004 8:01 PM
Reply to: Message 12 by Chiroptera
01-09-2004 7:49 PM


quote:
No, spontaneous generation is when fully formed organisms, usually already well-known species, are produced directly from rotting matter or from non-living matter - maggots from rotting meat, mice from decaying straw, and so forth.

Spontaneous generation applied to single-celled organisms too, such as bacteria. In fact, that's what Pasteur helped refute...remember? And you include "from non-living matter" in your explanation (which is correct).

So according to spontaneous generation, it was thought that the simplest living matter known could arise from non-living matter. That description of spontaneous generation fits the broad definition offered for abiogensis given in this thread” “Abiogenesis is the generation of living matter from non living matter.”, “It is a beginning without life (from non life to life)”; “the development of living organisms from non-living matter.”

A good definition of abiogenesis should be given: one that clearly distinguishes it from spontaneous generation.

[This message has been edited by DNAunion, 01-09-2004]


This message is a reply to:
 Message 12 by Chiroptera, posted 01-09-2004 7:49 PM Chiroptera has replied

Replies to this message:
 Message 15 by Chiroptera, posted 01-09-2004 8:05 PM DNAunion has replied
 Message 16 by Loudmouth, posted 01-09-2004 8:10 PM DNAunion has replied

DNAunion
Inactive Member


Message 17 of 415 (77444)
01-09-2004 8:13 PM
Reply to: Message 15 by Chiroptera
01-09-2004 8:05 PM


quote:
Bacteria are well developed organisms. They are not necessarily the simplest life possible.

So?


This message is a reply to:
 Message 15 by Chiroptera, posted 01-09-2004 8:05 PM Chiroptera has replied

Replies to this message:
 Message 20 by Chiroptera, posted 01-09-2004 8:19 PM DNAunion has replied

DNAunion
Inactive Member


Message 19 of 415 (77446)
01-09-2004 8:19 PM
Reply to: Message 16 by Loudmouth
01-09-2004 8:10 PM


quote:
These are a little rough around the edges, feel free to nit pick.

Spontaneous generation: Common species found on the earth today can be produced from inanimate chemicals, such as muddy puddles (frogs), meat left out in the sunlight (maggots and flies), or milk left in a jug for a long period of time (lactobacillus). No new species can be created from spontaneous generation, but instead the theory describes where they come from.

Abiogenesis: A self propagating chemical reaction starts that results in self replicating polymers. This gives rise to more complex chemical reactions due to accretion of small mistakes in the self replication reactions. Eventually, this results in cellular life due to capture in lipid bodies, followed by diversification into the species we see today.


That's good. I think in the other thead some stressed time a little more. That is, if we still believed in spontaneous generation we would believe that organisms were arising spontaneously all around us today - it would be a continuous, ongoing process. On the other hand, abiogenesis is believed to have occurred only "once", several billion years ago.

Anyway, I think the person who wanted to know what abiogenesis was will not now confuse it with spontaneous generation.


This message is a reply to:
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DNAunion
Inactive Member


Message 21 of 415 (77450)
01-09-2004 8:21 PM
Reply to: Message 18 by Chiroptera
01-09-2004 8:15 PM


quote:
In this age of mad-cow disease, think prions: is a prion living or non-living?

Non-living.


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DNAunion
Inactive Member


Message 22 of 415 (77451)
01-09-2004 8:22 PM
Reply to: Message 20 by Chiroptera
01-09-2004 8:19 PM


And that's why the definitions for abiogenesis needed to be improved by eliminating such a possibility as bacteria arising spontaneously, fully formed, from non-living matter.

[This message has been edited by DNAunion, 01-09-2004]


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DNAunion
Inactive Member


Message 24 of 415 (77508)
01-10-2004 12:20 AM
Reply to: Message 23 by sidelined
01-09-2004 10:45 PM


What I think? Okay, I think it's a researcher vastly exagerating his work, just as he has always done.

This message is a reply to:
 Message 23 by sidelined, posted 01-09-2004 10:45 PM sidelined has replied

Replies to this message:
 Message 25 by sidelined, posted 01-10-2004 12:37 AM DNAunion has replied

DNAunion
Inactive Member


Message 26 of 415 (77574)
01-10-2004 12:47 PM
Reply to: Message 25 by sidelined
01-10-2004 12:37 AM


Yes, I could...but won't.

If I can't get people here to accept something as self-evident and non-controversial as "DNA contains information", even after weeks of trying - using multiple dozens of posts explaining the logic and also supporting the position with tons of material from various mainstream college texts, then what chance do I have of getting a fair hearing on this matter?

[This message has been edited by DNAunion, 01-10-2004]


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DNAunion
Inactive Member


Message 28 of 415 (77730)
01-11-2004 10:53 AM
Reply to: Message 27 by Quetzal
01-11-2004 8:41 AM


quote:
I more or less agree with DNAunion that the particular research cited in the essay is somewhat overblown.

Yes. And let's not forget that, although not explicitly stated in web page linked to, among Fox's claims is to have created actual life - honest-to-goodness living cells - from non-life in the lab, under prebiotically plausible conditions.

He should have left it at something like, "I've created protein-like molecules that can form somewhat cell-like aggregates under conditions that I and some others personally feel are prebiotically plausible. The formation of these macromolecules and their aggregate spheres may have been one step in a multi-step path that lead from non-life to life here on Earth". I guess Fox didn't find the "truth" to be sensational enough.

[This message has been edited by DNAunion, 01-11-2004]


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DNAunion
Inactive Member


Message 30 of 415 (77827)
01-11-2004 4:32 PM
Reply to: Message 29 by sidelined
01-11-2004 1:55 PM


I'll give you some introductory thoughts.

There is good circumstantial evidence that RNA would have come before proteins, and that proteins would have come before DNA. So the general outline for the appearance of the main biological macromolecules would have been RNA -> proteins -> DNA.

But RNA is a tough molecule to make under prebiotic conditions - nothing even close to success has been reported. So it's hard to get an RNA World in the first place. On the other hand, it's fairly easy to get amino acids, and from there it's not implausible to have gotten some "multimers" of them to form prebiotically. Perhaps non-coded "proteins" played a role in helping to establish the RNA World, after which the standard RNA -> protein -> DNA path took over. However, without being coded, there would be no genetic continuity between "generations" of these "proteins"...so how could a population of specific "proteins" be maintained? How could they have evolved? It would appear each "generation" would just be a start-from-scratch collection of random sequences.

Maybe RNA wasn't the first replicator.

Possibly there is a molecule simpler than, but very much like, normal RNA that was the first self-replicator. After it was established, some series of slight compositional "mutations" could then have produced genuine RNA: which might have been a better self-replicating molecule and so have "taken over", starting the standard RNA -> protein -> DNA path. But is there a molecule simpler than, but very much like, RNA that can self-replicate? None have been found so far.

Perhaps the simpler molecule was nothing like RNA. But then how did the transition from nothing-like-RNA to RNA occur? That's problematic.

Perhaps metabolism was the first part of life to arise. But how can a closed metabolic cycle form spontaneously under prebiotically plausible conditions? It almost assuredly wouldn't have occurred in solution, with the substances floating around freely in the ocean. Perhaps the substances were all concentrated on a mineral surface, such as near a hydrothermal vent? Is such a scenario plausible? Depends upon which OOL researcher you ask: Wachtershauser says it is; Orgel says that it isn't. Has it been demonstrated in the lab? No.

[This message has been edited by DNAunion, 01-11-2004]


This message is a reply to:
 Message 29 by sidelined, posted 01-11-2004 1:55 PM sidelined has replied

Replies to this message:
 Message 31 by sidelined, posted 01-11-2004 4:51 PM DNAunion has replied

DNAunion
Inactive Member


Message 32 of 415 (77856)
01-11-2004 7:04 PM
Reply to: Message 31 by sidelined
01-11-2004 4:51 PM


There is evidence that indicates that scientists will eventually be able to direct the synthesis of an RNA molecule capable of self-replication. They've managed to create one that can copy about 14 bases of itself using direted evolution: but the molecule itself is about 180 based long so there's still quite a way to go. However, it is possible that it is just a single (or a few) problem that is stopping the process and once it is (they are) solved the way from 14 all the way up to 180+ will be clear sailing. I don't see any reason to believe that with the success they've had so far that it is literally impossible for an RNA molecule to self-replicate: I'd say it's almost a certainty. The real question is, what is the minimal complexity required? What if it ends up that the RNA molecule must be 250, or 350, nucleotides long? What is the probability that such a molecule would have formed by chance alone on the prebiotic Earth? If it is far too low to be plausible, then an RNA first scenario would be wiped out.

But that would still leave open the pre-RNA possibilities. Perhaps a simpler molecule could self-replicate, and was therefore able to evolve some complexity. This pre-evolved complexity that RNA would somehow overtake would eliminate the total reliance upon chance. But how would the transition take place? If the original pre-RNA molecules are different from RNA, then their three-dimensional conformations would differ too. Since catalytic function - such as self-replication - is dependent upon three-dimensional shape, and the two molecules' would differ, why should be expect the transition to retain the ability to self-replicate?

As has been the case ever since OOL research started, there's a lot of "maybe"s, "what if"s, "could be"s, and so on.

The origin of life is a mystery - and intriguing puzzle. What's the solution? Well, if someone is looking for some scientific proof that abiogenesis is impossible, it's not there. If someone is looking for a complete scientific explanation for how life actually could have originated, it's not there either.

Speculation by either side is fine, but if someone misrepresents scientific facts, then they should be corrected. Arguments based on invalid premises can't be trusted to be correct. (This final paragraph was not addressed to anyone in particular).

[This message has been edited by DNAunion, 01-11-2004]


This message is a reply to:
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DNAunion
Inactive Member


Message 34 of 415 (78299)
01-13-2004 9:32 PM
Reply to: Message 33 by Quetzal
01-12-2004 8:36 AM


quote:
There are two that I can think of (although others have been proposed) - peptide RNA aka pRNA or peptide nucleic acid aka PNA.

Both PNA and pRNA are possible precursors for genuine RNA, but pRNA is pyranosyl RNA, not peptide RNA. The primary difference between genuine RNA and pRNA is that biological RNA has a five-membered furanosyl ring, while pRNA has a six-membered pyranosyl ring.

quote:
And a final ref on my favorite PNA:

Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, 1996 "A self-replicating peptide" Nature, 382:525-8

quote:
--------------------------------------------------------------------------------
The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.
--------------------------------------------------------------------------------


That article discusses a modified natural protein, not PNA (which is completely artificial and has nitrogeneous bases, like a nucleic acid).

So far so good: but here comes the part where everyone usually gets their panties all tied up in a wad...

The molecule they used CANNOT actually self-replicate. I have a long “essay” explaining why it can’t, and I might have even posted it at this site before (it comes up a lot and I can't remember where all I've discussed it). Anyway, I will go into the gory details if anyone wants me to.

[This message has been edited by DNAunion, 01-13-2004]


This message is a reply to:
 Message 33 by Quetzal, posted 01-12-2004 8:36 AM Quetzal has replied

Replies to this message:
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DNAunion
Inactive Member


Message 37 of 415 (78514)
01-14-2004 9:21 PM
Reply to: Message 36 by Brad McFall
01-14-2004 3:29 PM


Re: ?
quote:
conceptually or evidentially?? If you say both I will have said that both Gould and I made the same scaling error or deviation from variation when thinking of Whitman's claim contra De Vries and Darwin on not how the Leopard but the Pigeon got it's spots that...if there IS NOT a cicularity in reasoning to the larger clade then evidence will show that Gould was mistaken in series what I would be in sequence. Gould did it conceptually in that case and me "if"NOTGOULD or either/or evidentarily. We all know how to spell super-natural...

Are you a Saturday Night Live fan? Do you remember the sketch where Phil Hartman was playing Frank Sinatra, who was hosting a talk show with guests: Sting was playing Billy Idol, one of the women on the show was wearing a "Bald wig" and pretending to be Sinead O'Connor, and Chris Rock was playing some rapper (sorry, not into rap so I can't remember the name)? Ring a bell? Do you remember what Phil Hartman's character kept saying to Chris Rock's character? Well, I am saying that to you.


This message is a reply to:
 Message 36 by Brad McFall, posted 01-14-2004 3:29 PM Brad McFall has replied

Replies to this message:
 Message 38 by Brad McFall, posted 01-15-2004 5:24 PM DNAunion has replied

DNAunion
Inactive Member


Message 39 of 415 (78716)
01-15-2004 6:38 PM
Reply to: Message 38 by Brad McFall
01-15-2004 5:24 PM


Re: ?
But the protoplasmic oscillator will transcend the diversity of spatial correlation, rendering the quanta of distribution, whether intrinsic or extrinsic, reducible to maximum entropic wavelets seathing through the vaccuum of space time continuum, as per Einstein's normalistic characterization of sublime entanglement of virtual photon pairs, manifesting marcoscale pertubations, which, in turn throw open the corridor of possibility to consciouness escaping the confines of empirical enprisonment of time dilation, generating ultra-scale fluxs of lumeniferous ether strings, whose vortices wind around spacetime, engulfing, as it were, the essense of protoplasm itself.

Ooops, mispoke. In the last part, that should be, "generating ultra-scale fluxs of lumeniferous ether strings whose cardinality implies prime manifestation of the principles of quantum electrodynamics, and whose vortices...". Left out that key part.

[This message has been edited by DNAunion, 01-15-2004]


This message is a reply to:
 Message 38 by Brad McFall, posted 01-15-2004 5:24 PM Brad McFall has replied

Replies to this message:
 Message 40 by Brad McFall, posted 01-20-2004 11:17 AM DNAunion has taken no action
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