Transition from chemistry to biology

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.

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

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So?

Sounds good to me, Loudmouth.I should also add, that spontaneous generation seems to be the belief that living organisms can arise directly from non-living matter. This is not abiogenesis, since every description of abiogenesis seems to imply that there is a chain of descent from definitely non-living matter to something that we would call living, but the intermediate stages may be hard to classify as either "living" or "non-living". (In this age of mad-cow disease, think prions: is a prion living or non-living? How about an ordinary virus?)

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

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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.

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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.

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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.

The development of fully formed bacteria from non-living matter would be a case of spontaneous generation, which, as you point out, was discredited by Pasteur. It is not a case of abiogenesis, since none of the proposals for abiogenesis that I am aware of suggests that bacteria ever arose directly from non-living matter.

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

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Non-living.

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]

Hello folks.Just a quick line to drop off a website address. Check it out and let me know what you think. Page Not Found - HolySmoke!

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

DNACould you explain your contention?

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]

Side:I more or less agree with DNAunion that the particular research cited in the essay is somewhat overblown. Or at least, doesn't go into enough detail on what the problems are with proteinoid microspheres being the LUCA precursor. One of the key problems is that there has been little or no evidence produced that these microspheres self-replicate. Although there have been a wide variety of different kinds of microsphere produced, there's no indication that they reproduce themselves - one of the critical capabilities that the first "critter" had to have.Note, however, that Fox's proteinoids (or more acurately thermal proteins) very likely could have formed the first protocell - and may have served as a template or "home" for the self assembly of more complex polypeptides.Anyway, for a look at what these things are, you can get no better than the source, Fox himself.Przybylski AT, Fox SW, 1984 "Excitable artificial cells of proteinoid", Appl Biochem Biotechnol 10:301-7

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The proteinoid cells are assembled of thermal polymers of amino acids. Typically, an appropriate mixture of amino acids containing aspartic or glutamic acid is heated at 190 degrees C for 6 h, stirred with water for 2 h, dialyzed during 2 d, and lyophilized. Spheroidal cells are made from such polymer by dissolving it in the water by boiling, and then cooling. Many of them can be made by sonication at room temperature. These artificial cells, ranging from microns to tens of microns in diameter (depending on composition and preparation), have double membranes and various internal compositions. The spherules can microencapsulate dyes, oxidant-reductant compounds or acceptor-donor substances, and can be packed together. Such spherules display electrical polarization and electrical discharges and respond to intra- and extracellular ionic and electric influence upon membrane and action potential. These properties arise from the double membrane structure, asymmetric membrane permeability, and channeling phenomena. Such features as exponential dependence of the steady-state conductance and capacitance as well as negative resistance of the membrane seem to be responsible for the flip-flop alternations of the membrane polarization, rhythmic electric oscillations, and all-or-none action potentials. The presence of such chromophores as pteridine and flavin in polymers constituting these cells is responsible for their photosensitivity.

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Fox's original paper isn't on line, but if anyone wants a reference:Fox SW, Jungck JR, Nakashima T 1974, "From proteinoid microsphere to contemporary cell: formation of internucleotide and peptide bonds by proteinoid particles", Orig Life 5:227-37.I still prefer an RNA or pRNA or PNA First scenario for abiogenesis, probably at a submarine thermal vent or cracking front, but Fox's microspheres could be the first cells.

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

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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]

Quetzal and DNAunionThanks for the critique of Fox. I do find it easier to work from the position of the weaknesses of a persons explanation for things since it allows me a chance to ascertain for myself how strong their work actually is.Quetzal mentioned a position for how abiogenesis occured but DNA did not.So I would like to understand what it is you view as weaknesses in your own scenarios and what would be required in order to resolve the difficulties.

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"I am not young enough to know everything. "
Oscar Wilde

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]