[jimbrook]

I posted the following in the undergrad general chem forum, but then I realized it probably belongs here. 
Most of you are probably aware of the DNA/protein dillema - DNA is required to synthesize protein, but protein is required for the transcription or replication of DNA.  Evolutionists sidestep this problem by saying there was an "RNA world" initially, wherein RNA spontaneously formed, and was capable of self-replication, which then evolved to the DNA model with which we are now familiar.  It has been said that a 50 nucleotide string of RNA would be required for self-replication.  I was recently reviewing general chemistry, as part of my overall continuing education as a doctor.  When I reviewed thermodynamics, and particularly the concept of Gibbs free energy, the following question hit me:  What is the Gibbs free energy of formation for a 50 nucleotide strand of RNA?  If anybody has ever figured that out, it would give us a quantitative measurement of the spontaneity of such a reaction.  Has anybody ever done the calculations?  I would not know how to do it, but I speculate that the value would be overwhelmingly large and positive, as such a molecule has a very high degree of order.  Correspondingly, I suspect that the equilibrium constant that would be derived from this information would be vanishingly small, 10 to the power of some very large negative number.  I do not know how to type a "delta" character, so instead I will use "&"   
&G = &H - T&S is the equation for Gibbs free energy, and from that we get &G = -RT ln K
Does anybody know anybody who might have some of this quantitative information on the plausibility of the "RNA world" ever having developed?  It seems to me that thermodynamics would disprove evolution.  Maybe somebody should do the research, but it just might rock the boat a bit.

[Yggdrasil]

The change in Gibbs free energy for the formation of RNA from nucleoside triphosphates is negative meaning that the process occurs spontaneously (else, how would the process occur in cells?).  However, the formation of nucleoside triphosphates from ribose, nucleobases, and inorganic phosphate is not spontaneous.  How these molecules would form in an abiotic world is still an open question that many scientists have considered. 

Note that it is still possible for non-spontaneous reactions (i.e. those rxns with a positive change in free energy) to occur if an external source provides energy from the reaction.  One common thought is that ultraviolet radiation (or other cosmic radiation) could cause these reactions to occur on a prebiotic world.

[renge ishyo]

It is well known that the probability of complex ordered life emerging on its own from a pool of random chemicals is ridiculously small. The real problem isn't even in the energetics of the bond breaking or making (as Yggdrasil points out, it is known that you can use certain nucleotide monomers to make RNA polymers); the real problem is the *order* inherent in the DNA language itself (the specific sequence of nucleotides) that gives the molecule its functions. You can supply energy to make RNA spontaneously copy itself even if the  :delta: G for the formation is unfavorable. In fact, a study released this year showed that it was possible for short RNA sequences to self replicate from monomers in a test tube given the proper environment (see the April 2009 issue of Scientific American). Again though, the RNA in this case was order specific (i.e. not a random sequence), and the order at the core of the replication was not produced from randomness (the experimenters placed the nucleotides in a specific order to carry out the experiment). So this was an impressive step in the direction of an "abiotic" theory, but not confirmation by any means.

The problem is "what" is going to put the nucleotides in a specific order in the polymer to begin with so that they can behave in a specific way? The probability of a specific order of nucleotides, such as those in our own DNA, arising from a pool of random chemicals is vanishingly small. Does that mean it can't happen? NO...in fact, what the mathematics tell you is that it most certainly *can* happen, but that the odds of it happening are just very unlikely. This isn't only a problem of biology, the probability of the whole universe developing in just the way it did is ridiculously small too. Don't think these small probabilities put the scientist in a more uncomfortable position to explain the origin of life than that of the theologist. The probability that other modern creation theories are true based on current scientific understanding is very low as well...

These particular questions (as I am sure you are well aware) are hard to discuss seriously in a formal manner because the issues are corrupted by political interests. Neither side can "prove" their case because there isn't enough evidence at present to conclude definitively one way or the other. Notice I said at present. There have been many times in the past where "politically controversial" scientific theories in Biology akin to modern evolutionary theory were hotly contested due to a lack of experimental evidence to decide the issue one way or another. For instance, take the case at the turn of the 20th century with vitalism. There was a group arguing that life required a special living "vital force" in order to carry out all the life sustaining chemical reactions in the body. Then there was a second group arguing that chemical reactions in the body could take place in the same way that they occur with inorganic matter and that living "vital forces" were unnecessary.

If you notice, this debate was quite similar to the one taking place with the "abiotic" theory of evolution today. One side argues that there must be some "special" thing to it, the other argues that it can take place without any "special" thing required. There were plenty of theoretical arguments supporting both sides (some proponents of vitalism were even very prominent scientists at the time, including Louis Pasteur!). In this case however, it was found in the early 1900s that you can carry out biological reactions in a test tube without a living "vital force" present (this arrived with the discovery of enzymes which catalyze such reactions and clearly appear to be "non-living" entities, operating on physical and chemical principles, when studied in a test tube). Now both sides agree that biochemical reactions can occur without the "vital force" to help them along, so they are merely arguing about the same issue somewhere else! (actually, the "vital force" turned out to be DNA as you need that to make the enzymes...this didn't help the vitalists case however, because DNA quickly turned out to be a "non-living" molecule, operating on physical and chemical principles, just like the enzymes were).

I'm not mentioning the vitalism argument to wave it in anybody's face, it is just a good example of why it is a good idea to wait for the results of experiments to ultimately decide these issues and not merely produce more and more pointless theoretical arguments in favor of one side or the other. In the meantime, I think the lesson to be learned here is it is best for both groups of people to keep an open mind about things (but humans rarely do what is best for them ^^).

[doc30]

Thermodynamics and evolution are quite consistent with each other. The are mistakes made by people simply trying to calculate probabilities of a given sequence arising because they neglect the basic physics behind the formation of the chemical entities in question.

For example, there is a very low probability of a specific 50 unit sequence of RNA assembling spontaneously, but that is not how the reaction works. It can be described as a polymerization of a mixture of a small number of monomers that grows through the addition of a single monomer or through the addition of a shorter chain of RNA.

Secondly, when the building blocks of RNA are mixed where they can link together, it is inevitable that chains of different sequences will arise, even though the probability of each specific sequence is vanishingly small.

Once chain growth gets started, the appearance of one chain that can catalyze self replication, even if imperfectly, will very quickly lead to an accumulation of such sequences since these would be more favored. Once replication is initiated, the basic tenants of evolution through natural selection would apply. Note that abiogenesis and evolution are not the same theory and are quite different areas of study.

And getting back to thermodynamic discussions, the basic chemistry between any two units is roughly similar. So the idea that there is a thermodynamic prohibition against chain growth is essentially an argument againt polymerization.

Here is a link that discusses the probability of a specific sequence forming on an early Earth and illustrates the fallacies with creationist probability discussions.
http://www.talkorigins.org/faqs/abioprob/abioprob.html