Originally Posted By: Orac
So what Ilya is doing is literally equating life as an explosion. So if we take that out the more complex an organism the further from equilibrium it is and the more pressure it took to get it there.

That is about as layman as I can write it and we can expand it from there and discuss implications as we need.

Firstly, lets be clear - I don't need the layman's description. In my lab we study (among other things) the spontaneous formation of membrane microdomains, using GP Gladyshev's model of Prigoginean thermodynamics as our analytical basis. So instead of the lame (and factually incorrect) laymans descriptions, lets actually talk about the science.

Secondly, you've not dealt with the problems that your original claims vis-a-vis QM entropy are still wrong, and the new article you does not support your contention that higher complexity = farther form thermodynamic equilibrium.

Finally, you've completely mis-represented (i.e. lied) about what Prigoginean thermodynamics says about biological systems. It says nothing relating to complexity. What it actually says is the further something is from thermodynamic equilibrium the more pressure there *should* be to return to equilibrium. Since this doesn't happen with life, you need to invoke processes such dissipative structures to explain the apparent stability off of thermodynamic equilibrium. These are what allow you to maintain a state of non-equilibrium (i.e. life), through dissipating entropy to the external environment.

Originally Posted By: Orac
Originally Posted By: ImagingGeek

2) you (and AFAIK, all physicists) have yet to demonstrate that QM processes operate at any measurable level at the macromolecular level of biology.

And that is where I just start rolling my eyes and realise how little you know of QM.

The atoms in your biology is based on QM, the reactions and there rate are controlled by QM and as far as we know all energy in every system ever studied from black holes and suns to galaxies and the universe can be defined by it's equations.

If you're rolling your eyes, than your grasp of QM is poorer than mine. QM processes such as superposition, entaglment, quntatization, etc, are not observed in macromolicules; indeed, atoms quite often don't exhibit these behaviours. How to explain the loss of quantum coherence in larger structures, and how group behaviours lead to decoherance, has been for over 50 years the single greatest unanswered question in QM.

Originally Posted By: Orac
I would also point out that when you biologists actually bother to start looking for QM effects funny how you find them

The initial discovery of QM in photosynthesis

We have found a whopping total of 1 - in a system evolved to efficiently capture photons. It is, and remains, the only such system known. And its arguable if coherence explains it - the counter argument has been forster energy transfer, which is as explanative an explanation. You've presented one half of an ongoing debate and claimed it as 'proof'. That is quite dishonest.

And, I'd point out, that showing one biological structure that has evolved to pass on electron excitation energy is a far cry from demonstrating that QM processes involved in QM models of entropy - coherence, entanglement, etc - have measurable impacts on biological polymers.

Originally Posted By: Orac
It appears you are still claiming there is only one theory for the driver of evolution can I please get a link or description to that so I can read and study it.

So you're arguing against evolutionary theory without being familiar with it?

A few books that cover the basics:
The Greatest Show on Earth: The Evidence for Evolution by Richard Dawkins

The Tangled Bank: An Introduction to Evolution by Carl Zimmer

There are a lot more, but those are two of my favourite "introductory"-type books. They give a pretty good summation of the basic theory, but do not go into the more technical aspects such as quantifying selection, etc.

Originally Posted By: Orac
3.)Types of evolution

From the above you seem to be seperating out different types of evolution micro,macro etc and in your final added comment you are now even seperating creation of life (Abiogenesis).

I never used the term 'types of evolution', so I have no idea what you are talking about. I did discuss the outcomes of evolution - i.e. adaptive vs. neutral vs. maladaptive. I also discussed positive vs negative selection. But those are all evolution, not different kinds.

I would never separate macro from micro - they are simply different quantities of the same thing. All evolutionary biologists will tell you that abiogenesis is a separate science, driven by different processes, than evolution. Confounding the two is a common creationist tactic. I'd direct you to the above two books for an explanation of the issue.

Originally Posted By: Orac
I find the last seperation interesting in that by your own discussion you can't have evolution until things can replicate and you even claim they are driven by different energetics.

Could you elaborate on your theory of how this all works?

I should refine my answer by saying "potentially driven by other energetics". Replication is a pre-requisite for evolution, as by definition, evolution is 'descent with modification'. If you cannot replicate - and replicate imperfectly, you cannot evolve. As for elaboration, it is simple.

Abiogenesis involves three processes: 1) the formation of biopolymers (protein, RNA, DNA, lipids, etc), 2) the formation of energy-generating processes (i.e. metabolism) and 3) the combination of 1 & 2 into a self-replicating system.

The formation of monomers and polymers happens spontaneously, following classical chemical thermodynamics - things react, you end up with products with lower free energy, Gibbs is happy. However, the formation of these into complexes & structures doesn't necessarily obey Gibbs free energy or use conventional biological mechanisms (due to a lack of metabolism); meaning that these higher-order structures rely on emergent properties - i.e. Prigogine's dissipative structures.

Originally Posted By: orac

Originally Posted By: John Desmond Bernal

Stage 1: The origin of biological monomers
Stage 2: The origin of biological polymers
Stage 3: The evolution from molecules to cell

Bernal suggested that evolution commenced between Stage 1 and 2

And I would agree - sort of. One of the more accepted models of abiogenesis is the RNA world model; essentially, RNA (which forms spontaniously under abiotic conditions) polymerizes, a small portion of those are (by chance) ribozymes capable of self-replication, and thus can 'evolve'. However, this 'evolution' is limited to the ribozymes; it will not 'extend' to associated molecules or metabolic pathways - i.e. there is no phenotype or selective advantage at the level of any proto-organism. The formation and incorporation of non-ribozymes would still be a simple stoichastic process not involving replication, modification or inheritance. More biologists place the beginning of evolution at the proto-cell stage; the step where metabolic processes are also genetically encoded, encapsulated in a cell-like structure, and thus there is a pseudo-organism capable of inheritance, modification and phenotypes.

Originally Posted By: orac
Anyhow clearly I am wrong according to you so lets first deal with the great biology view of it all.

But you're wrong about (or deliberatly misrepresenting) the physics as well, so we're still at zero...