For fluffy :-)
Rather than continue hijacking the_leander's threads, I figured it would be rather better to create one...
So, going back to this one, lets take a stock check. Existing evolutionary models explain the diversification and origin of new species of entire organisms relatively well. I have no issue with this at all.
For me, as we have discussed, the problem is the biochemical level. Prebiotic chemistry is a fascinating area that I studied intensely for a while. Foregoing for a moment the argument about how it all started, let's think about it for a moment.
It seems to me that there has been no significant (bio)chemical evolution for a very, very long time. What do I mean by this? Well, there may be small improvements in cell chemistry here and there, but by and large your human internal cellular machinary is not far in advance of any other eukaryotic organism - just look at yeast and you will find the same chemistry going on. Eukaryotes are themselves a step up from prokaryotes that have new biochemical pathways added on top of the prokaryotic set but do not significantly change those they inherited.
If you look at the most primitive forms of viral life you can find (and arguably they are not even really living), you find that they still use the same chemistry. They still use at least RNA to store their compositional make up and they use protein casings etc.
It seems therefore, that the biochemical complexity known today is largely unchanged in every organism known. Were still using the same nucleic acids, proteins, electron transport chains, photosynthetic systems since pa(ramecium) fell of the bus (to paraphrase X-Ray). Of course there are better examples of some metabolic systems, but fundamentally the chemistry has not changed.
This is one reason I don't think that existing evolutionary theory (as it applies to biology) applies to the chemistry that enables the biology to exist.
If we consider that biological evolution is taking place all around us, why do we not observe the same in chemistry? Once you have a self replicating, sustainable chemical system there is no reason to assume it would be completely replaced by a more efficient one, just as bacteria still exist in profusion, despite being biologically usurped by more sophisticated organisms competing for the same resources.
If the existing evolutionary models apply to chemistry, why are there no pre - nucleic acid / protein chemstry based organisms known? Just because the latter may be more efficient, the former system(s) capable of self replication should still exist. Yet none do.
So, the biochemistry we know - that is nucleic acid / protiens / sugars / redox / electron transport / photosynthesis - has been around relatively unchanged since life began, despite the vast changes in the biology it has enabled. In fact, the only variations we see are in how that chemisrty sources the energy it needs in order to drive itself (be it photosynthesis, iron-sulfur, carboyhdrate oxidation etc).
There is no evidence that the chemistry itself was ever any less sophisticated; there are no rival self-replicating chemistries known, no evidence any have ever existed and no evidence that the existing biochemistry has changed significantly or is changing. In short there is no tangible evidence of "chemical evolution".
So the questions remain. Where did the present chemistry come from and how did it establish itself so quickly given that it appears to have moved so little since? After all, it is generally believed the first single celled organisms powered by this chemistry were happily replicating wihin 200 million years of conditions being favourable.
There are many other reasons why I don't believe the existing evolutionary paragdims (as applied to biology) apply to the underlying chemistry, the above are just a few.
In my opinion, there is so much more to discover - sticking to creationalism or darwinism are not going to get us far.
If the_leander is reading this, feel free to hijack - it is only fair :-D
