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Author Topic:   Transition from chemistry to biology
sidelined
Member (Idle past 4294 days)
Posts: 3435
From: Edmonton Alberta Canada
Joined: 08-30-2003


Message 31 of 415 (77834)
01-11-2004 4:51 PM
Reply to: Message 30 by DNAunion
01-11-2004 4:32 PM


DNAunion

You state

But then how did the transition from nothing-like-RNA to RNA occur? That's problematic

Is there any evidence that points to the mechanism that allows RNA to replicate?


This message is a reply to:
 Message 30 by DNAunion, posted 01-11-2004 4:32 PM DNAunion has responded

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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]


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Quetzal
Member (Idle past 4258 days)
Posts: 3228
Joined: 01-09-2002


Message 33 of 415 (77948)
01-12-2004 8:36 AM
Reply to: Message 31 by sidelined
01-11-2004 4:51 PM


Side,

I concur with DNAunion in both post 30 and 32. I'd like to add that all of the current abiogenesis hypotheses have weakenesses, so like he says, we haven't (yet?) been able to cover the last couple of gaps. Also, as he noted, there are rather significant problems with assuming full-blown RNA is the "first" replicator. Simpler, more stable molecules would appear to me to be more likely. There are two that I can think of (although others have been proposed) - peptide RNA aka pRNA or peptide nucleic acid aka PNA. PNA especially is quite stable, doesn't require the complex ribose sugars (which are problematic to synthesize in adequate quantities under most of the plausible pre-biotic conditions).

In addition, DNAunion mentioned the possibility that other molecules or substances could have assisted the formation of complex polymers. Cairns-Smith is the person credited with coming up with the idea that clays - because of their catalytic properties - may have provided a template or even catalyzed the formation of early complex polymers. Of course, this has problems as well - for instance clays don't necessarily form a lattice or matrix that is ideally designed for the assembly of biologically significant macromolecules.

Anyway, one of the bigger problems with abiogensis research up to now is that most researchers have concentrated on one hypothesis pretty much to the exclusion of everybody else's ideas. My "gut feeling" is that the final solution is going to be a synthesis of several different approaches.

A few references, of the hundreds on the subject:

Lazcano A, Miller SL, 1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time” Cell vol 85:793-798

Martin W, Russell MJ, 2002 "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" The Royal Society: Philosophical Transactions: Biological Sciences 358:59-85

In addition, further to what DNAunion mentioned about RNA autocatalysis, one relevant reference is:

Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP 2001, "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension", Science, 292:1319-25

quote:
The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

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.

This message is a reply to:
 Message 31 by sidelined, posted 01-11-2004 4:51 PM sidelined has not yet responded

Replies to this message:
 Message 34 by DNAunion, posted 01-13-2004 9:32 PM Quetzal has responded

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:
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Replies to this message:
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Quetzal
Member (Idle past 4258 days)
Posts: 3228
Joined: 01-09-2002


Message 35 of 415 (78352)
01-14-2004 7:13 AM
Reply to: Message 34 by DNAunion
01-13-2004 9:32 PM


Thanks for the corrections. Type in haste... Anyway, as my daughter always says, "I knew that..."

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Brad McFall
Member (Idle past 3418 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 36 of 415 (78451)
01-14-2004 3:29 PM
Reply to: Message 1 by sidelined
01-04-2004 5:19 PM


?
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...

[This message has been edited by Brad McFall, 01-14-2004]


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

Brad McFall
Member (Idle past 3418 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 38 of 415 (78702)
01-15-2004 5:24 PM
Reply to: Message 37 by DNAunion
01-14-2004 9:21 PM


Re: ?
No, but I might be if I got cable. I asked the question and I hope that Sideline-d will answer it directly for then I will try to "discuss" rather than 'circle the wagons'. What it did recall was my first web posting that I made on Taxacom but I know this has not the precision that has subsequently been established here. The link is
<http://listserv.nhm.ku.edu/cgi-bin/wa.exe?A2=ind0102&L=TAXACOM&P=R5038&D=1&O=D> and I have about 24 posting there that show that even the professionals could only keep up with my Lamarkian style of speculative argumentation for so long but still as this is chemsitry to biology you will see that I have been trying to talk about biology (protenomics and genomics TO chemistry) and from basis I might be able to discuss a few things in this thread.

Here is a little bit of those "older" textual things:

"I propose to use the virial to solve the conundrum in the term 'biological informatics' whether or not it rotates genetics in a new revolution and takes nostalgia back to a time before the distinction of bio-informatics was taken for the metaphase plate of geneticists or not and only is of service in a routable computer network of biological information.

Every gene in it's Mendelian instantiation will have a virial. These virials will build partial pressure by pressure the relation of genomic and protenomic informatics to the level of chemisty. Biochemistry begins with some free path these gene-virials have spatially available that eventually are cast in GIS areally co-extensive sets logically setting the stage from recognition of Some hierarchy to the organismic tissue-organ-cell level where upon acoustic/image processing and pre-DNA style genetics begin to not object to morphometrics; multitasking up to the graphic anatomy of the systematist generally but because with the expanded taxonomy that visualizations have provided the taxa specialist and the best-guess-species-location algorithm(s) by combining GIS(species and habitat layers), the impetus socially providing for l-commerce spins up to a biodiversity object web that from conservation and alpha taxonomy creates the deductive biogeography irregardless of time as in the style of Euclid and Newton but as part of morphogeny with or without virtual reality that is psychologically needed to move beyond "

I would be able to talk about WAXweb in this external channel but I know others here like to keep the techic stuff to a minimum so if I know if it is not going to be an issue c v e for BOTH evidence and concept I could give it a try else I will be content to understand that that in CGI the environment variable is "inherited" and thus how P likely got C for E!


This message is a reply to:
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Replies to this message:
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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:
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Brad McFall
Member (Idle past 3418 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 40 of 415 (79554)
01-20-2004 11:17 AM
Reply to: Message 39 by DNAunion
01-15-2004 6:38 PM


Re: ?
will it? (will it transcend????). this doesnt look that sublime to me.

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q3psycho
Inactive Member


Message 41 of 415 (82839)
02-03-2004 8:03 PM
Reply to: Message 39 by DNAunion
01-15-2004 6:38 PM


Re: ?
I think you need a tranquilizer mr. DNAunion.

If they produce life in the lab then they will have proved that life can be produced in the lab. From there we can deduce the minimum intelligence necessary to produce life from pre-existing materials God left around for us.

So its sort of like when your children learn how to get cereal out of the cupboard and milk from the fridge to make their breakfast. it's really nice to see that, but it represents a very limited amount of IQ power in comparison to providing those things in the first place.


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Gup20
Inactive Member


Message 42 of 415 (106626)
05-08-2004 3:22 PM


The two basic ingredients in living things is DNA molecules and protein molecules. DNA is a long string of repeated units called nucleotides or bases. A protein molecule is a long string of amino acids. In all forms of life, the sequence of DNA you inherit tells the cells how to line up amino acids to make each of the proteins responsible for structure and function. So the cell takes a look at the genetic code and says “ok there are these three beads of DNA over here… I’ll line up one amino acid over here...” and continues checking back and forth.

Well what about that relationship? Is that what you would expect by time chance and chemistry? At first you might say so because after all DNA is a string of bases, protein is a string of amino acids, and nothing is more natural then the reaction between acids and bases. So the evolutionist says “see – if you just wait long enough, bases will start lining up amino acids and life will begin just by time chance and chemistry, no creator is needed”. Exactly the opposite [is true]. The problem is that natural relationship between bases and acids is the wrong one as far as living things are concerned.

Bases and acids react alright – but when? At death! What is [biological] death anyway? It is the triumph of chemistry over biology. As soon as molecules in your body begin doing what they want to chemically, you begin to “return to the dust from which you are taken”. In DNA the bases stick out along the side of the chain. IN proteins the acids are part of the chain. If you let DNA and protein do what come naturally, it actually contributes to the aging process and finally the decomposition and destruction of life.

The living relationship, the one we need for living things, is using a series of bases taking 3 at a time to line up a series of amino acid R groups. Those groups can be acids… but they can also be base! Single ring, double ring, short chain, long chain, with or without sulfur – they can be almost anything chemically. The point is this – there is no natural tendency for a series of bases to line up a series of R groups. That relationship has to be imposed from the outside. At this fundamental level, then, we have evidence that life on earth is a product of special creation.

by: Dr. Gary Parker (doctorate in biology)
Author of 5 Biology Textbooks
Creation Scientist
(from the video "Evolution to Creation" from Answers in Genesis)


Replies to this message:
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sidelined
Member (Idle past 4294 days)
Posts: 3435
From: Edmonton Alberta Canada
Joined: 08-30-2003


Message 43 of 415 (106630)
05-08-2004 3:51 PM
Reply to: Message 42 by Gup20
05-08-2004 3:22 PM


Gup20

The living relationship, the one we need for living things, is using a series of bases taking 3 at a time to line up a series of amino acid R groups. Those groups can be acids… but they can also be base! Single ring, double ring, short chain, long chain, with or without sulfur – they can be almost anything chemically. The point is this – there is no natural tendency for a series of bases to line up a series of R groups. That relationship has to be imposed from the outside. At this fundamental level, then, we have evidence that life on earth is a product of special creation.

The relationships need not be imposed from outside as again it is the atomic level at which the rules of physics define the relationships that chemistry imposes upon the biological.The error here is assuming that the fundemental processes occur at the level of "living" things. Again there is bias on the part of people to consider the word life has a basis in reality that arises somehow magically seperate from the atoms that make it up.This is not clearly shown to be so and if we do not have a clear picture of what life is then why are we arguing for it.


"We cannot define anything precisely! If we attempt to, we get into that paralysis of thought that comes to philosophers, who sit opposite each other, one saying to the other, 'You don't know what you are talking about!' The second one says 'What do you mean by know? What do you mean by talking? What do you mean by you?', and so on."

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SUnderwood
Inactive Member


Message 44 of 415 (111163)
05-28-2004 2:13 PM
Reply to: Message 15 by Chiroptera
01-09-2004 8:05 PM


It always was, always is and alway will be
Interesting.

Why Transitions FROM and TO? Why not just "It is as it was, and has always been".

Life (as we perceive it) is a consequence of design/happenstance.

The transition from chemistry to biology is a phenomenon that is only apparent in the mind of you, the reader.

Biology is chestry, is physics, is mechnics, is quantum physics. The Universe and its "features" does not categories, but some features tend to dance together, in an interesting "life" like way.

Sean.


This message is a reply to:
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sidelined
Member (Idle past 4294 days)
Posts: 3435
From: Edmonton Alberta Canada
Joined: 08-30-2003


Message 45 of 415 (111566)
05-30-2004 1:12 PM


I am going to bump this topic by reinterating my original question which seems to have been lost in a fog along the line.

Why is it not within the realm of possibilty that chemical elements in proper combinations and enviroment can give rise to living organisms without the need for supernatural intervention?

I would like to concentrate on debating this without going off on a tangent.

This message has been edited by sidelined, 06-01-2004 06:36 PM


"Science is the belief in the ignorance of experts. "

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