Sunday, 5 October 2014

Another Creationist Lie Refuted By Science

Early bioenergetic evolution

Here's another one of those scientific papers that creation pseudoscience frauds must dread because it deals with another of their mysterious 'beginnings', abiogenesis.

Beginnings are such things as the Big Bang, the origins of morality and abiogenesis, or, as creationists like to call it, life from no-life. These are where they can fool those ignorant of science that the beginning must have had a magic cause because there couldn't have been something before it so, to the scientifically illiterate (i.e. creationists), it looks like getting something from nothing. They then leave parochial ignorance and cultural arrogance to do the rest for them safe in the knowledge that their victims will always conclude that the only magic cause on offer is the locally popular god.

This is why the Big Bang, the beginnings of morality and abiogenesis all feature so prominently in their apologetic but abiogenesis is where they get themselves into a real fix because they need to reduce it to something even their victims can understand, so they talk about a thing called 'life' as though it's a real, material, measurable thing like a Universe or a fundamental particle that 'those mad/dishonest/Satanic scientists' think just popped up from nowhere. They also need to remain consistent with their idiotic claim that the Second Law of Thermodynamics means evolution is impossible, so the last thing they want their victims knowing is that decreased entropy is perfectly possible in an open system and that life is actually all about local entropy reduction. Hence 'life' has to be presented as some sort of vague magicky ingredient.

Of course, as I've explained before, about the only thing that can be regarded as 'life' is the ability of a system to overcome locally the tendency toward decreasing order (known to physics as increased entropy) by utilising a source of energy. This was reinforced recently by another science paper which said pretty much the same thing when discussing how self-replicating systems could have evolved in hot seabed volcanic vents. This latter paper set out to resolve a paradox in abiogenesis theory which I'll try to briefly summarise here:
  • Basics to all living systems is a process which takes energy and build a molecule of ATP from a phosphate molecule and ADP. This ATP is then available as an energy store to drive metabolic processes. It's analogous to charging a battery so the battery can then supply electricity to do work. This process is basically the same in all living things, even bacteria and archaea and so is assumed to have been present in the Last Universal Common Ancestor (LUCA).
  • The process takes place inside a membrane, with a proton pump to pump hydrogen ions (protons) to the outside, so the pressure this concentration difference produced gives the pressure for protons to flow back in again through protein enzymes in the membrane which then catalyse the reaction to produce the ATP. This depends (or was assumed to depend) on an impermeable membrane. However, archaea have a different membrane structure to everything else.
  • Neither bacteria (and their evolutionary descendants) nor archaea could have restructured their membranes while keeping the system intact).
Calm down creationists; this isn't an example of irreducible complexity. The paradox was resolved by showing that an inefficient but workable process could have evolved with an imperfect membrane, so both bacteria and archaea could have evolved their own solution to this inefficient process, ending up with two different type of membrane.

Now this paper, by a mixed European team of researchers led by Filipa L. Sousa from the Institute of Molecular Evolution, University of Düsseldorf, Germany have shown in detail how this could have happened before even the membranes themselves had evolved. The evolution of the membrane could have been the final step which allowed living systems to break free from the substrate in which they had already evolved this energy extraction process and self-replication.

Incidentally, this paper was drawn to my attention by PZ Myers in his excellent Pharyngula blog. It is also freely available under Creative Commons licence.

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution.

Note that definition of 'life' in the opening sentence. Can anyone see any need for magic in that description of chemistry and physics, or any reason why it involves some special form of either, making living systems materially different to the rest of matter?

So here we have a very plausible mechanism whereby a self-replicating system could have evolved out of the chemicals present and in the conditions of a hot hydrothermal ocean vent, progressing through an RNA stage to a DNA-based replication system and evolving the basic metabolic processes whilst still inside cavities in the acreations produced by the vents, with no need at that stage to evolve cell membranes. However, when those membranes did form, it enabled the early 'cells' to break free and become free-living systems with the basic entropy management and self-replicating system in place.

Now, this doesn't need to be the final word on the subject because this is just one plausible mechanism by which the first free-living systems could have taken half a billion years to evolve. For the creationist claim that "scientists can't explain the origin of life from no-life", however, science like this is fatal because all science need do is to outline a plausible mechanism to be able to explain it. And this, or any, plausible mechanism only needs to have occurred once. With maybe billions of similar processes happening for maybe half a billion years, even the very unlikely has a high probabilities of occurring at least once.

The reaction of creation pseudoscience frauds will be the traditional ones, of course: they will either lie about it, misrepresent it, attack the scientists or, most likely and most frequently these days, ignore it altogether and rely on their victims' refusal to read anything which might shake their 'unshakeable' faith in magic.

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